ARTICLE | doi:10.20944/preprints201911.0247.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: glycoside hydrolase; glycan; phylogenetic profiling
Online: 21 November 2019 (04:46:13 CET)
Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy, and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3), and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.
ARTICLE | doi:10.20944/preprints202309.0533.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Cycas; chloroplast genome; phylogenetic analysis; SSR; large repeats
Online: 7 September 2023 (10:31:06 CEST)
Cycas (family Cycadaceae), spread throughout tropical and subtropical regions, is crucial in con-servation biology. Due to the subtle morphological variations between species, a solid spe-cies-level phylogeny for Cycas is lacking. Because of the rapid progress in high-throughput se-quencing technology, it has become feasible to acquire complete chloroplast (cp) genome se-quences, which provide a molecular foundation for phylogenetic research. In the present study, we employed next-generation sequencing technology to assemble and analyze the chloroplast genomes of six Cycas plants, including their genome structure, GC content, and nucleotide di-versity. The Cycas chloroplast genome spans 162,038 to 162,159 bp and contains 131 genes, in-cluding 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Through a comparative analysis, we found that the chloroplast genome of Cycas was highly conserved, as indicated by the contraction and expansion of the inverted repeat (IR) re-gions and sequence polymorphisms. In addition, several non-coding sites (psbK-psbI, petN-psbM, trnE-UUC-psbD, ndhC-trnM-CAU, and rpl32-trnP-GGG) showed significant varia-tion. The utilization of phylogenetic analysis relying on protein-coding genes has substantiated the division of Cycas primarily into four groups. The application of these findings will prove valuable in evaluating genetic diversity and the phylogenetic connections among closely related species. Moreover, it will provide essential support for the advancement of wild germplasm re-sources.
ARTICLE | doi:10.20944/preprints201807.0330.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Globin-like superfamily, Phylogenetic analysis, Taxonomic tree
Online: 18 July 2018 (11:11:36 CEST)
Globin-like superfamily constitutes a superfamily of both extracellular and intracellular proteins that are found in 3 kingdoms of life. Globins are respiratory proteins that usually bind an oxygen molecule .Earlier, phylogenetic study of globin like superfamily was based on morphological character, however, molecular basis of their functional diversity is not completely understood. The present study focuses on the phylogenetic analysis of globin at molecular level. Firstly, proteins of SCOP families of globin like superfamily were retrieved from NCBI and then similar proteins are retrieved from PSI BLAST results and then pfam was used to predict the domains and two domains: Globin and Phycobilisome were analysed. Other analysis predicted the localization in cytoplasm of most of the proteins. The nucleotide sequences of same species for protein analysis were retrieved from NCBI, and phylogenetic analysis of aligned fasta files of proteins and nucleotides by using MEGA at molecular level was performed and analysis shows the difference on taxonomic tree and phylogenetic tree.
SHORT NOTE | doi:10.20944/preprints202002.0310.v1
Subject: Biology And Life Sciences, Virology Keywords: 2019-nCoV; phylogenetic tree; phylogenetic profile
Online: 23 February 2020 (02:32:54 CET)
Background: The seventh novel human infecting Betacoronavirus that causes pneumonia (2019 novel coronavirus, 2019-nCoV) originated in Wuhan, China. The evolutionary relationship between 2019-nCoV and the other human respiratory illness-causing coronaviruses is unclear. We sought to characterize the relationship of the translated proteins of 2019-nCoV with other species of Orthocoronavirinae.Methods: A phylogenetic tree was constructed from the genome sequences. A cluster tree was developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The combined data were used to characterize the relationship of the translated proteins of 2019-nCoV to other species of Orthocoronavirinae.Results: Our analysis reliably suggests that 2019-nCoV is most closely related to BatCoV RaTG13 and belongs to subgenus Sarbecovirus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus. The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins. Clade 1 consisted of a group of conserved proteins in Orthocoronavirinae comprising Orf1ab polyprotein, Nucleocapsid protein, Spike glycoprotein, and Membrane protein. Clade 2 comprised six proteins exclusive to Sarbecovirus and Hibecovirus. Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. Thus, we speculate that knowledge of the functional changes in the NS7b and NS8 proteins during evolution may provide important information to explore the human infective property of 2019-nCoV.
ARTICLE | doi:10.20944/preprints202309.0179.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: nepovirus; RNA2 sequences; phylogenetic and recombination analyses
Online: 4 September 2023 (14:30:57 CEST)
Despite its remote discovery (1977) and numerous reports of its presence in vari-ous plant species in many countries, the available molecular information for the artichoke Italian latent virus (AILV) is still limited to a single complete genome sequence (RNA1 and 2) isolate from grapevine (AILV-V) and to a partial sequence portion from RNA2 of an isolate of unknow origin and host, both reported in the GenBank. Here we report the results of molecular analyses conducted on RNA2 of AILV isolates, sequenced for the first time in this study, together with the first-time finding of AILV in a new host plant species, i.e., chard (Beta vulgaris subsp. vulgaris). The different AILV isolates sequenced are from artichoke (AILV-C), gladiolus (AILV-G), sonchus (AILV-S) and chard (AILV-B). At the bio-logical level, the AILV-B was found to be involved with vein clearing and mott-ling symptoms on chard leaves. At the molecular level, sequencing results of RNA2 segments showed that AILV-C, AILV-G, AILV-S and AILV-B were 4,629 nt in length (excluding the 3’ terminal polyA tail), hence one nt shorter than that of AILV-V reported in the GenBank. The comparative sequence analysis between the CR of RNA2 of all isolates showed that AILV-V was the most variable isolate, with the lowest sequence identities of 83.2% and 84.7% at the nucleotides and amino acids levels, respectively. Putative intra-species sequence recombination sites were predicted among the AILV isolates, of which the AILV-V, AILV-C and AILV-B genomes were found to be mostly involved. This study adds further mo-lecular information on the previously unrecorded high genomic variability of the Nepoviruses of subgroup B, together with information on recombinations that may have conditioned the infection and transmission of AILV in nature; thus learning the way forward to design a new integrated pest management of chard plantation.
ARTICLE | doi:10.20944/preprints202009.0663.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ORFV; PCR; Sanger method; B2L gene; Phylogenetic analysis
Online: 27 September 2020 (04:58:03 CEST)
Aim: Despite the endemic nature of contagious ecthyma in Nigeria, there is limited report on the molecular characterization of the isolates responsible for disease outbreaks. The aim of this study was to molecularly characterize ORFV isolated from clinical infections in goats in Sokoto metropolis. Materials and Methods: Seronegative embryonated chicken eggs were used to isolate ORFV via the chorio allantoic membrane (CAM) route according to the established protocol. Viral DNA was extracted from infected CAM and the full coding region of B2L gene was amplified by PCR and subsequently sequenced by Sanger’s method. The nucleotide sequence results were blasted for identification and phylogenetically analyzed using MEGA and Bioedit softwares. Results and Discussion: The results showed that B2L gene sequences of the ORFV UDUS/01/19/More strain showed slight variability (96- 98.7%) with the reference sequences. Our isolate clustered within the same clade with Korean strain signifying a close genetic relationship. Unique amino acid substitutions were noted in our isolate when compared with other references. This is arguably the first genetic characterisation of B2L gene of ORFV circulating in Nigeria. Conclusion: Our study has provided in sight into the genetic diversity of ORFV in the study area. This is crucial for the design of effective vaccines against the disease which are currently lacking in the country.
ARTICLE | doi:10.20944/preprints201609.0048.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: oligopeptide transporters (OPTs); Medicago truncatula; phylogenetic analysis; gene express
Online: 15 September 2016 (08:39:23 CEST)
Oligopeptide transporters (OPTs) are a group of membrane localized proteins that have a broad range of substrate transport capabilities and contribute to numerous biological processes. However, limited information has been reported on OPTs in higher plants. In this study, a comprehensive analysis of the OPT gene family in Medicago truncatula was performed. A total of 26 OPT genes (MtOPT01-MtOPT26) have been identified in the Medicago truncatula genome. Phylogenetic analyses indicated that MtOPTs consisted of two distinct subgroups, 12 MtOPTs belonged to the peptide transport subgroup (PT-OPT) based on their predicted amino acid sequences containing the two highly conserved motifs (NPG and KIPPR) and 14 MtOPTs belonged to yellow stripe subgroup (YS-OPT). The MtOPTs distributed on each of 8 chromosomes in Medicago truncatula. Sequence analysis verified that MtOPTs significant similar to those in other plants. The copy number of MtOPTs was low and the multiply of MtOPTs was simple relatively. Gene structure analysis showed that most of the MtOPTs have various numbers of introns. The multiple of MtOPTs might play different biological roles which were supported by the fact that MtOPTs have a distinct tissue-specific expression pattern. The data obtained in this study will help to better understand the complexity of the MtOPTs gene family and provide new evidence for the function and evolution of the OPT gene family in higher plants.
ARTICLE | doi:10.20944/preprints202311.0626.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: chloroplast genome; comparative genomics; Eusideroxylon; Lauraceae; phylogenetic relationships
Online: 9 November 2023 (10:11:45 CET)
In our article in Genome Biology Ecology six years ago, one complete plastid genome of Belian was assembled for comparative analyses of the plastomes in Lauraceae. However, Ariati et al. (2023) concluded that our sequenced Belian individual could be located in the clade of Myristicaceae instead of that of Lauraceae. Here, we performed re-analyses of additional two Belian plastomes, along with 42 plastomes from plants spanning ten families of the Magnoliids. The plastomes of the three Belian individuals range from 157,535 to 157,577 bp in length. Comparative genomic analysis revealed 170 mutation sites in their plastomes, which include 111 substitutions, 53 indels, and six microinversions. Phylogeny was reconstructed using maximum likelihood and Bayesian approaches for 44 magnoliids species indicated that our three Belian individuals are nested among the species in the family Lauraceae rather than Myristicaceae.
ARTICLE | doi:10.20944/preprints202306.1166.v1
Subject: Biology And Life Sciences, Virology Keywords: human papillomavirus 58; E7 oncogene; variants; phylogenetic analysis; gene expression
Online: 16 June 2023 (10:01:35 CEST)
Cervical cancer is associated with persistent infections by high-risk HPV types that may have nucleotide polymorphisms and, consequently, different oncogenic potentials. Therefore, the objective of this study was to evaluate the genetic variability and structural effects of E7 oncogene of HPV58 in cervical scraping samples from Brazilian women. The study was carried out with patients from hospitals in metropolitan area of Recife, PE, Brazil. The most frequent HPV type was HPV16, 18 and 58, respectively. Phylogenetic analysis showed that the isolates were classified as sublineages A2, C1 and D2. Two positively selected mutations were found in E7: 63G and 64T. The mutations G41R, G63D and T64A in E7 protein were predicted to reduce the stability of the protein structure. Regarding the interaction of the E7 variant of HPV58 with the signaling of the NF-kB pathway, we observed that the variant HPV58/UFPE-54S decreased the activity of the pathway when compared to the prototype and the other variants behaved similarly to the prototype and the prototype increased the activity of the pathway when compared to pcDNA. In this study, it was possible to identify mutations that may interfere in the molecular interaction between the viral oncoproteins and host proteins.
ARTICLE | doi:10.20944/preprints202306.0088.v1
Subject: Biology And Life Sciences, Virology Keywords: Canine; feline; chaphamaparvovirus; codon usage; phylogenetic; cross-species transmission
Online: 1 June 2023 (12:26:50 CEST)
Chaphamaparvovirus (ChPV) is an ancient virus that has been detected in a variety of hosts. In this study, based on the phylogenetic analysis and the adaptability of ChPV to multiple hosts, we evaluated the potential of feline (FeChPV) and canine ChPV (CaChPV) for cross-species transmis-sion. Phylogenetic analysis showed that FeChPV and CaChPV were closely related. Notably, two strains of ChPVs isolated from domestic cats and 2 from dogs clustered together with CaChPVs and FeChPVs, respectively, suggesting the stringent boundaries between canine and feline ChPV may be broken. Further analysis revealed that CaChPV and FeChPV were more adapted to dogs than to cats, strongly suggesting the possibility of unidirectional or bidirectional transmission be-tween dogs and cats. Mutation analysis identified several shared mutations in cross-species-transmissible strains that were not located within immune epitopes. Furthermore, the VP struc-tures of FeChPV and CaChPV exhibited a high degree of similarity across both cross-species-transmissible and non-cross-species-transmissible strains. However, definitive experimental evi-dence is lacking, and its capacity for cross-species transmission should be approached with cau-tion and elucidated in further studies.
ARTICLE | doi:10.20944/preprints201809.0611.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: LRR-RLK family; Gossypium; expansion; phylogenetic analysis; gene expression profile; stress defense
Online: 30 September 2018 (16:18:37 CEST)
Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been reported to play important roles in plant growth, development and stress responses. However, no comprehensive analysis of this family has been performed in Gossypium, which are important economic crop and suffer various stresses in growth and development. Here we conducted a comprehensive analysis of LRR-RLK family in four Gossypium species (G. arboreum, G. barbadense, G. hirsutum and G. raimondii). A total of 1641 LRR-RLK genes were identified in the four Gossypium species involved in our study. Maximum-likelihood phylogenetic tree revealed that all the LRR-RLK genes were divided into 21 subgroups. Exon-intron organization structure of LRR-RLK genes kept relative conserved in subfamilies and between Arabidopsis and Gossypium. Subfamilies XI and XII were found dramatically expanded in Gossypium. Tandem duplication acted as an important mechanism in expansion of Gossypium LRR-RLK gene family. Function analysis suggested that plant hormone signaling and plant-pathogen interaction pathway were enriched in Gossypium LRR-RLK genes. Promoters analysis and expression profiles analysis revealed that Gossypium LRR-RLK genes were extensively regulated by TFs, phytohormone and various environmental stimuli, and play key roles in stress defense and diverse development processes. Our study provided valuable information for further function study of Gossypium LRR-RLK genes.
ARTICLE | doi:10.20944/preprints202005.0396.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; variant analysis; phylogenetic analysis; viral evolution
Online: 24 May 2020 (18:25:47 CEST)
The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral genome is an RNA virus consisting of approximately 30,000 bases. As part of testing efforts, whole genome sequencing of human isolates has resulted in over 1,600 complete genomes publicly available from GenBank. We have performed a comparative phylogenetic analysis of the sequences, in order to detect common mutations within the population. Analysis of variants occurring within the assembled genomes yields 417 variants occurring in at least 1% of the completed genomes, including 229 within the 5’ untranslated region (UTR), 152 within the 3’UTR, 2 within intergenic regions and 34 within coding sequences.
ARTICLE | doi:10.20944/preprints202202.0295.v2
Subject: Biology And Life Sciences, Plant Sciences Keywords: Alfalfa; bZIP transcription factor; phylogenetic analysis; expression pattern; abiotic stress
Online: 27 March 2023 (08:37:10 CEST)
Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies such as differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus, and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa. In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in Arabidopsis thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physicochemical properties, motif analysis, and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that particular bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought, and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. These expression patterns were further verified by qRT-PCR. However, further functional characterization of bZIP transcription factors in alfalfa will help illuminate the role they play in stress tolerance mechanisms in legumes and facilitate the molecular breeding of stress tolerance in alfalfa.
ARTICLE | doi:10.20944/preprints201907.0119.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Endophytic fungi, Leptosphaerulina chartarum; Curvularia trifolii; mitogenomes; gene content; phylogenetic implications
Online: 8 July 2019 (12:44:35 CEST)
In tobacco plants, symbiont endophytic fungi are widely distributed in all tissues where they play important roles. It is therefore important to determine the species distribution and characteristics of endophytic fungi in tobacco. Here, two parasitic fungi Leptosphaerulina chartarum and Curvularia trifolii were isolated and identified from normal tobacco tissue. We sequenced the mitogenomes of these two species and analysed their features, gene content, and evolutionary histories. The L. chartarum and C. trifolii mitochondrial genomes were 68,926 bp and 59,100 bp long circular molecules with average GC contents of 28.60% and 29.31%, respectively. The L. chartarum mitogenome contained 36 protein coding genes, 26 tRNA genes, and 2 rRNA genes (rrnL and rrnS), which were located on both strands. The C. trifolii mitogenome contained 26 protein coding genes, 29 tRNA genes, and 2 rRNA genes (rrnL and rrnS). The L. chartarum 26 tRNAs ranged from 70 bp to 84 bp in length, whereas the 29 tRNAs in C. trifolii ranged from 71 bp to 85 bp. L. chartarum and C. trifolii mtDNAs had an identical mitochondrial gene order and orientation and were phylogenetically identified as sisters. These data therefore provide an understanding of the gene content and evolutionary history of species within Pleosporales.
ARTICLE | doi:10.20944/preprints202110.0246.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Chloroplast genome; Machilus leptophylla; Hanceola exserta; Rubus bambusarum; Rubus henryi; Simple sequence repeat; Phylogenetic analysis
Online: 18 October 2021 (14:30:50 CEST)
The chloroplast genome is conservative and stable, which can be employed to resolve genotypes. Currently, published nuclear sequences and molecular markers failed to differentiate the species from taxa robustly, including Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. In this study, the four chloroplast genomes were characterized, and then their simple sequence repeats (SSRs) and phylogenetic positions were analyzed. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. Moreover, the chloroplast genomes contained typical four regions. Six classes of SSR were identified from the four chloroplast genomes, in which mononucleotide was the class with the most members. The types of the repeats were various within individual classes of SSR. Phylogenetic trees indicated that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed under family Ocimeae. Additionally, R. bambusarum and R. henryi were clustered together, whereas they did not belong to the same species due to the differing SSR features. This research would provide evidence for resolving the species and contributed new genetic information for further study.
ARTICLE | doi:10.20944/preprints202308.1167.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: COVID-19; SARS-COV-2; Omicron Variants; Phylogenetic tree; Genome Sequence
Online: 16 August 2023 (07:47:50 CEST)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in humans in Wuhan City at the end of December 2019. Since then, it has spread to all the countries. Therefore, global interest has been focused on discovering treatments and developing successful vaccines. This study sequenced the complete genome of the SARS-COV-2 Omicron Omicron (BA.1) and sub-variants (BA.1.1, BA.2), which were isolated from 40 individuals in Duhok, Iraq. Ninety-five different mutations were identified when the complete genome of the SARS-COV-2 virus discovered in Wuhan, China (accession number: NC 045512.2) was matched to the virus sequence using sequencing technology (Illumina, USA). Sequence analysis revealed 38 mutations in spike glycoprotein (S), 30 of which were found in ORF1a. Additionally, 11 mutations were found in ORF1b, and 7,3,2,1 mutations were found in Nucleocapsid (N), membrane protein (M), Open Reading Frames 6 (ORF6), Open Reading Frames 9 (ORF9), and Envelope (E) genes, respectively. Phylogenetic analysis and transmission further confirmed that the isolates found in Iraq had distinct infection origins and were closely related to those from other countries and states. According to the findings of this study, a new vaccine can be developed based on identifying new Omicron variant mutations and sub-variants such as BA.2, which were identified for the first time in Iraq.
ARTICLE | doi:10.20944/preprints202304.0961.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19 patient; whole Genome sequence; Of SARS-COV-2; phylogenetic analysis and Transmission supported
Online: 26 April 2023 (05:15:36 CEST)
Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in people in the city of Wuhan at the end of December 2019, and it has since spread to all continents. Global interest has been focused on discovering a treatment and developing a successful coronavirus vaccine as a result of the emergence of this new coronavirus. In this research, we sequenced the whole genome of the SARS-COV-2 virus that were isolated from 40 patients in Duhok, Iraq. 95 different mutations were identified in our isolation when such the whole genome sequence of the SARS-COV-2 isolated from the city of Wuhan, China (Accession number: NC 045512.2) was matched to the virus's sequence using Sequencing technology (Illumina , USA ) and Assembly method (iVar 1.3.1). Sequence analysis revealed that 38 mutations were found at spike glycoprotein (S), 30 of which were found in the ORF1b , 11 mutations were found in ORF1b ,7,3,2,1 mutations were found in ( N,M,ORF6 ,ORF9 /E ) genes which had been linked to structural changes at various places. The conclusion that the cases in Iraq were of different origins of infections and had a close relationship with the isolates from different country and state were further confirmed by phylogenetic analysis and transmission. The whole genome sequence of the SARS-CoV-2 , which were identified from the Iraqi Kurdistan region, and reported as a first study in Kurdistan region.
ARTICLE | doi:10.20944/preprints202305.0285.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Epidemiology; Wastewater-based Epidemiology; Phylogenetic Analysis; Machine Learning Approach; Molecular virology
Online: 5 May 2023 (03:31:35 CEST)
The COVID-19 pandemic has posed a significant global threat, leading to several initiatives for its control and management. One such initiative involves wastewater-based epidemiology, which has gained attention for its potential to provide early warning of virus outbreaks and real-time information on its spread. In this study, water samples from two wastewater treatment plants (WWTPs) located at the south east of Spain (Region of Murcia) namely Murcia, and Cartagena, were analyzed by RT-qPCR, Phylogenetic Analysis, and Machine Learning Approach. The aim was to determine whether SARS-CoV-2 detection in the WWTPs of these two cities could serve as a proxy for the virus's spread in the population. The results confirmed that the levels of SARS-CoV-2 in these wastewater samples changed concerning the number of SARS-CoV-2 cases detected in the population and variant occurrences were in line with clinical reported data. Additionally, the phylogenetic analysis showed that samples obtained in close sampling times exhibited a higher similarity than those obtained more distantly in time. A second analysis using a machine learning approach based on the mutations found in the SARS-CoV-2 spike protein was also conducted. Hierarchical Clustering (HC) was used as an efficient unsupervised approach for data analysis. Results indicated that samples obtained in October 2022 in Murcia and Cartagena were significantly different, which corresponded well with the different virus variants circulating in the two locations. The proposed methods in this study are adequate for comparing the Accumulated Natural Vector (ANV) of the SARS-CoV-2 sequences as a preliminary evaluation of potential changes in the variants that are circulating in a given population at a specific time point.
ARTICLE | doi:10.20944/preprints202107.0094.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Phyllanthaceae; Phyllanthus; Leptopus; transition and transversion substitutions; chloroplast genome; phylogenetic; polymorphic loci; rps16 loss; atpF intron loss
Online: 5 July 2021 (12:03:13 CEST)
Family Phyllanthaceae is one of the largest segregates of the eudicot order Malpighiales and its species are herb, shrub, and tree, which are mostly distributed in tropical regions. Certain taxonomic discrepancies exist at genus and family level. Here, we report chloroplast genomes of three Phyllanthaceae species—Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius— and compare them with six others previously reported Phyllanthaceae chloroplast genomes. The species of Phyllanthaceae displayed quadripartite structure, comprising inverted repeat regions (IRa and IRb) that separate large single copy (LSC) and small single copy (SSC) regions. The length of complete chloroplast genome ranged from 154,707 bp to 161,093 bp; LSC from 83,627 bp to 89,932 bp; IRs from 23,921 bp to 27,128 bp; and SSC from 17,424 bp to 19,441 bp. Chloroplast genomes contained 111 to 112 unique genes, including 77 to 78 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) that showed similarities in arrangement. The number of protein-coding genes varied due to deletion/pseudogenization of rps16 genes in Baccaurea ramiflora and Leptopus cordifolius. High variability was seen in number of oligonucleotide repeats while analysis of guanine-cytosine (GC) content, codon usage, amino acid frequency, simple sequence repeats analysis, synonymous and non-synonymous substitutions, and transition and transversion substitutions showed similarities in all Phyllanthaceae species. We detected a higher number of transition substitutions in the coding sequences than non-coding sequences. Moreover, the high number of transition substitutions was determined among the distantly related species in comparison to closely related species. Phylogenetic analysis shows the polyphyletic nature of the genus Phyllanthus which requires further verification. We also determined suitable polymorphic coding genes, including rpl22, ycf1, matK, ndhF, and rps15 which may be helpful for the reconstruction of the high-resolution phylogenetic tree of the family Phyllanthaceae using a large number of species in the future. Overall, the current study provides insight into chloroplast genome evolution in Phyllanthaceae.
ARTICLE | doi:10.20944/preprints202303.0270.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: genome sequence; infectious bursal disease virus; Nigeria; phylogenetic analysis; poultry; segments A and B
Online: 15 March 2023 (07:49:33 CET)
Infectious bursal disease (IBD) is a viral poultry disease known worldwide for impacting the economy and food security. The disease is endemic in Nigeria, with reported outbreaks in vaccinated poultry flocks. To gain insight into the dynamics of infectious bursal disease virus (IBDV) evolution in Nigeria, near-complete genomes of four IBDVs were evaluated. Amino acid sequences in the hypervariable region of the VP2 revealed conserved markers (222A, 242I, 256I, 294I and 299S), associated with very virulent (vv) IBDV, including the serine-rich heptapeptide motif (SWSASGS). Based on the newly proposed classification for segments A and B, the IBDVs clustered in the A3B5 group (where A3 are IBDVs with vvIBDV-like segment A and B5 are from non-vvIBDV-like segment B) forming a monophyletic subcluster. Unique amino acid mutations with yet-to-be-determined biological functions have been observed in both segments. Amino acid sequences of the Nigerian IBDVs showed that they are reassortant viruses. Circulation of reassortant IBDVs may be responsible for the vaccination failures observed in the Nigerian poultry population. Close monitoring of changes in the IBDV genome is recommended to nip deleterious changes in the bud, through the identification and introduction of the most appropriate vaccine candidates and advocacy/extension programs for properly implementing disease control.
ARTICLE | doi:10.20944/preprints202305.0206.v1
Subject: Environmental And Earth Sciences, Ecology Keywords: Africa; forest; savanna; phylogenetic; diversity; transition
Online: 4 May 2023 (06:04:39 CEST)
In tropical Africa, forests and savannas are the two most widespread biomes and potentially represent alternative stable states with divergent species composition. A classic, but untested, hypothesis posited by White (1983) suggests that the transition zones between forests and savannas contain a floristically impoverished assemblage with few representatives from each biome. Further, the evolutionary dimension of diversity has received limited attention, despite its importance for understanding the biogeographic history of biomes. Here, we quantify species richness and several measures of evolutionary diversity in 1° grid cells, using c. 300K occurrence records of trees and shrubs combined with biome affiliation data for 3,125 species. We find that assemblages in transition zones hold fewer woody species than assemblages in forest and savanna zones, as posited by White. However, transition zones hold more phylogenetic diversity than expected given their species richness, whether one considers forest and savanna assemblages separately or together. We also show that the Congo basin forest has low levels of phylogenetic diversity given the number of species and highlight south-eastern African savannas as a centre of savanna woody species richness and phylogenetic diversity. Regions with high phylogenetic diversity given the number of both forest and savanna species were centred around the Dahomey Gap and Cameroon, mainly in transition zones. Overall, our study shows that even if floristically impoverished, transition zones lead to unexpectedly high evolutionary diversity, suggesting they are important centres of evolutionary innovation and diversification.
ARTICLE | doi:10.20944/preprints202309.0299.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: mobile genetic elements; Anti-microbial resistance; Klebsiella pneumoniae; Whole genome sequencing; integrons; plasmids; sequence types; phylogenetic analysis
Online: 6 September 2023 (04:28:45 CEST)
Conjugative transposons in Gram-negative bacteria have a significant role in the dissemination of antibiotic-resistance-conferring genes between bacteria. This study aims to genomically characterize plasmids and conjugative transposons carrying integrons in clinical isolates of Klebsiella pneumoniae. Genetic composition of conjugative transposons and phenotypic assessment of 50 multidrug-resistant K. pneumoniae isolates from Tertiary-care Hospital (SQUH), Muscat, Oman was investigated. Horizontal transferability was investigated by filter- mating conjugation experiments. Whole genome sequencing (WGS) was performed to determine the sequence type (ST), acquired resistome and plasmidome of integron-carrying strains. Class 1 integron was detected in 96% of isolates and among integron-positive isolates, 18 stains contained variable regions. Horizontal transferability by conjugation confirmed the successful transfer of integrons between cells and WGS confirmed their presence in conjugative plasmids. Dihydrofolate reductase (dfrA14) was the most prevalent (34.8%) gene cassettes in class 1 integrons. MLST analysis detected predominantly ST-231 and ST-395. BlaOXA-232 and blaCTX-M-15 were the most frequently detected carbapenems and beta-lactamases in sequenced isolates. This study highlighted the high transmissibility of MDR-conferring conjugative plasmids in clinical isolates of K. pneumoniae. Therefore, the wise use of antibiotics and the adherence to effective infection control measures are necessary to limit further dissemination of multidrug-resistant organisms.
ARTICLE | doi:10.20944/preprints202310.1966.v1
Subject: Biology And Life Sciences, Aquatic Science Keywords: Elongate loach; Cobititdae; mitochondria genome; phylogenetic analysis
Online: 31 October 2023 (03:00:06 CET)
Elongate loach (Leptobotia elongata) is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition, and the phylogenetic relationships of L. elongata inferred using protein-coding genes (PCGs). However, the detailed information about is limited. Therefore, in this study, we sequenced the complete mitochondrial genome of L. elongata and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis respectively. The complete mitochondrial genome of the L. elongata, together with those of 36 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and two non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, L. elongata shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other 5 Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with L. elongata forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobititdae species.
BRIEF REPORT | doi:10.20944/preprints202308.2029.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Helicobacter pylori; ureC; phylogenetic tree; gastric cancer
Online: 30 August 2023 (07:16:25 CEST)
Helicobacter pylori (H. pylori) is known to play a significant role in the development of peptic ulcer diseases and gastric cancer. Previous studies have reported the existence of polymorphism in the ureC gene of H. pylori. However, the relationship between genetic sequence variations in ureC and the pathogenesis of peptic ulcer diseases remains unclear. We aimed to investigate the associations between ureC sequence variations and the development of gastric ulcer and gastric cancer. PCR amplification and DNA sequencing to analyze ureC sequences, and conducted phylogenetic analysis using MEGA X software. Samples from Taiwanese patients with gastric ulcer and gastric cancer were included in this study. PCR was used to amplify the ureC gene from these samples, followed by DNA sequencing. The obtained sequences were then subjected to phylogenetic analysis using MEGA X software. In addition, ureC sequences from different geographical regions, including China and other countries, were included in the analysis for comparison. Analysis of the ureC se-quences from Taiwanese samples revealed that 6 out of 7 gastric ulcer samples clustered together in one group, while the sequences from 7 out of 8 gastric cancer samples were distributed across other groups. Phylogenetic analysis incorporating ureC sequences from different geographical regions showed that Taiwanese ureC sequences could be divided into two distinct groups, although the bootstrap values supporting this separation were low. Notably, the ureC sequences from China formed a distinct group with a high bootstrap value, separate from sequences from all other countries. There are two genotypes of ureC sequences present in Taiwanese samples, with one genotype showing a closer association with gastric cancer. Additionally, the ureC sequences from China appear to be unique and separate from those obtained from other countries, indicating the presence of genetic diversity in ureC sequences among H. pylori strains from different regions, potentially contributing to differences in disease outcomes. Further research is needed to elucidate the specific mechanisms by which ureC sequence variations may influence the pathogenesis of peptic ulcer diseases and gastric cancer.
ARTICLE | doi:10.20944/preprints201905.0056.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: phylogenetic inference; maximum likelihood; parallel processing; HPC
Online: 6 May 2019 (11:12:20 CEST)
RAxML-NG is a new phylogentic inference tool that replaces the widely-used RAxML and ExaMLtree inference codes. Compared to its predecessors, RAxML-NG offers improvements in accur-acy, flexibility, speed, scalability, and user-friendliness. In this chapter, we provide practicalrecommendations for the most common use cases of RAxML-NG: tree inference, branch supportestimation via non-parametric bootstrapping, and parameter optimization on a fixed tree topo-logy. We also describe best practices for achieving optimal performance with RAxML-NG, inparticular, with respect to parallel tree inferences on computer clusters and supercomputers. AsRAxML-NG is continuously updated, the most up-to-date version of the tutorial described inthis chapter is available online at: https://cme.h-its.org/exelixis/raxml-ng/tutorial .
ARTICLE | doi:10.20944/preprints201807.0553.v1
Subject: Biology And Life Sciences, Virology Keywords: adenovirus, western palaearctic bats, phylogenetic analysis, Spain
Online: 30 July 2018 (03:57:27 CEST)
In the context of long-term screening for viruses on Western Palaearctic bats, we tested for the presence of adenovirus 1.392 oropharyngeal swabs and 325 stool samples taken from 27 bat species. Adenoviruses were detected in 12 species of the Vespertilionidae and the Rhinolophidae families. Fifty positive respiratory and 26 positive stool samples were studied. Phylogenetic analyses of partial hexon protein and partial DNA-dependent DNA polymerase genes, indicate all these bat adenoviruses belong to the genus Mastadenovirus but without constituting a monophyletic cluster. According to genetic identities, the new groups are distinct to the previously described Bat mastadenovirus A and B species, and contribute with potentially new members. Our data support that diversity of Bat mastadenovirus is host-dependent and increase the knowledge of potentially pathogenic virus from bats. For human concerns this knowledge is an important Public Health issue due to the active role of bats as viral reservoirs.
ARTICLE | doi:10.20944/preprints202311.1518.v1
Subject: Medicine And Pharmacology, Tropical Medicine Keywords: SARS-CoV-2; genome; sequencing; phylogenetic analysis; Peru
Online: 23 November 2023 (11:07:09 CET)
Objective: To identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. Methods: nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which have been considered mild, moderate and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. Results: it was determined that during the period December 2020 and January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, B.1.111 circulated, lineage C.14 the most predominant with 76.7% (n=23/30), these lineages were classified in clade 20D mainly and also within clade 20B and 20A. On the contrary, the variants found in the second batch of samples of the period September – October 2021 were Delta Variant (72.7%), Gamma (13.6%), Mu (4.6%), Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J and 21I. Conclusions: This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.
ARTICLE | doi:10.20944/preprints202309.2043.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Avipoxvirus; molecular characterization; phylogenetic analysis; viral introduction; Portugal
Online: 29 September 2023 (08:32:26 CEST)
Avipoxvirus (APV), a linear dsDNA virus belonging to the subfamily Chordopoxvirinae of the family Poxviridae, infects more than 278 species of domestic and wild birds. It is responsible for causing the avian pox disease, which is characterized by its cutaneous and diphtheric forms. With a high transmission capacity, it can cause high economic losses and damage to the ecosys-tem. Several diagnostic methods are available and vaccination of birds can be an effective pre-ventive measure. To update the molecular characterization and phylogenetic analysis of viruses isolated in Portugal between 2017 and 2023, ten APV-positive samples were analyzed. A P4b gene fragment was amplified by PCR and the nucleotide sequence of the amplicons was deter-mined by Sanger sequencing. The sequences obtained were aligned using ClustalW, and a max-imum likelihood phylogenetic tree was constructed. With this study, it was possible to verify that the analyzed sequences are distributed in subclades A1, A2, B1, and B3. Since some of them are quite similar to others from different countries and obtained in different years, it is possible to conclude that there have been several viral introductions in Portugal. Finally, it was possible to successfully update the data on avipoxviruses in Portugal.
ARTICLE | doi:10.20944/preprints202111.0167.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: chloroplast genome; Compositae; phylogenetic incongruence; plastid DNA; Senecioneae
Online: 9 November 2021 (12:51:07 CET)
Plastid genomes are in general highly conserved given their slow evolutionary rate, thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridisation, both processes usually complicating systematic inferences. In this study, we have generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity, and repeat composition of these sequences. By comparing the whole plastome sequences obtained, we confirmed the double inversion located in the long single copy region, for most of the species analysed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also show that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae -as well as in the sister family Calyceraceae - are lacking the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, are overall consistent with the general consensus for the family’s phylogeny, while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.
BRIEF REPORT | doi:10.20944/preprints202103.0755.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: evolutionary divergence; phylogenetic analysis; transporter proteins; Leishmania major
Online: 31 March 2021 (09:55:35 CEST)
Transporter proteins, P-glycoprotein (P-gp) and P4ATPase-CDC50, are responsible for the transport of Miltefosine drug across cell membrane of a protozoan parasite Leishmania major. Mutations or change in activity of these proteins may lead to emergence of resistance in the parasite. Owing to the structural and functional importance of these transporter proteins, in this ppaper, we have tried to decipher the evolutionary divergence of these Miltefosine transporter proteins across different forms of life including Protists, Fungi, Plants and Animals. We retrieved 96, 207, and 189 sequences of P-gp, P4ATPase and CDC50 proteins respectively, across diverse variety of organisms for the conserved analysis. Phylogenetic trees were constructed for these three transporter proteins based on Bayesian posterior probability inference. The evolutionary analysis concluded that these proteins remain highly conserved throughout the species diversity but still substantial differences in the proteins for host (Homo sapiens) and parasite (L. major) were observed which have led in targeting these Miltefosine transporter proteins in a parasite specific manner.
CASE REPORT | doi:10.20944/preprints202009.0543.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetics； comparative genomics； phylogenetic analysis； osteopetrosis； CLCN7 gene
Online: 23 September 2020 (07:56:30 CEST)
Osteopetrosis is a group of rare inheritable disorders of the skeleton characterized by increased bone density. The disease is remarkably heterogeneous in clinical presentation and often misdiagnosed. Therefore, genetic testing and molecular pathogenicity analysis are essential for precise diagnosis and new targets for preventive pharmacotherapy. Mutations in the CLCN7 gene give rise to the complete spectrum of osteopetrosis phenotypes and are responsible for about 75% of cases of autosomal dominant osteopetrosis. In this study, we report the identification of a novel variant in the CLCN7 gene in a patient diagnosed with osteopetrosis and provide evidence for its significance (likely deleterious) based on extensive comparative genomics, protein sequence and structure analysis. A set of automated bioinformatics tools used to predict consequences of this variant identified it as deleterious or pathogenic. Structure analysis revealed that the variant is located at the same “hot spot” as the most common CLCN7 mutations causing osteopetrosis. Deep phylogenetic reconstruction showed that not only Leu614Arg, but any non-aliphatic substitutions in this position are evolutionarily intolerant, further supporting the deleterious nature of the variant. The present study provides further evidence that reconstructing a precise evolutionary history of a gene helps predicting phenotypical consequences of variants of uncertain significance.
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Chinese sacbrood virus; VP1; Apis cerana; Phylogenetic analysis
Online: 5 January 2020 (15:49:12 CET)
The Chinese honeybee (Apis cerana cerana) sacbrood virus (CSBV) causes death of larvae and colony collapse, and could damage the beekeeping industry in China. We sequenced complete genomes of CSBV strains derived from the Maerkang area, Wenjiang area, and Wanyuan area of Sichuan province of China. The genome length of CSBV strains from Sichuan was 8863bp, and it contained one complete Open Reading Frame of a gene with 8544 bp that encoded a protein with 2848 amino acids. The (G+C) % and (A+T) % composition ranged from 40.6 to 40.7 and 59.3 to 59.4, respectively. A phylogenetic tree was constructed using the three CSBV strains and previously reported SBV and CSBV sequences from other regions. We found that viral strains clustered based on their region of origin and host species. The genetic sequences of the CSBV strain from Maerkang were 98.7% and 99.6% similar to CSBV strains from Wanyuan and Wenjiang, respectively. In addition, CSBV from Maerkang had 88.4%-95.2% sequence similarity to previously published genomes of CSBV or SBV from other areas. The VP1 gene sequenced in our study had a 43 bp deletion compared to VP1 sequences of CSBV from other regions in Asia. We detected 10 antigenic determinants on the VP1 protein of CSBV form Aba. Our study provides new insight into the diversity of CSBV strains in China and may help with identifying methods to prevent infection of honeybee colonies.
REVIEW | doi:10.20944/preprints201703.0101.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: glucose transporter; GLUTs; chicken; avian; mammal; phylogenetic analysis
Online: 15 March 2017 (08:34:06 CET)
The GLUT members belong to a family of glucose transporter proteins that facilitate glucose transport across the cell membrane. The mammalian GLUT family consists of thirteen members (GLUTs 1-12 and HMIT). Humans have a recently duplicated GLUT member, GLUT14. Avians express the majority of GLUT members. The arrangement of multiple GLUTs across all somatic tissues signifies the important role of glucose across all organisms. Defects in glucose transport have been linked to metabolic disorders, insulin resistance and diabetes. Despite the essential importance of these transporters, our knowledge regarding GLUT members in avians is fragmented. It has been clear that there are no chicken orthologs of mammalian GLUT4 and GLUT7. Our examination of GLUT members in the chicken revealed that some chicken GLUT members do not have corresponding orthologs in mammals. We review the information regarding GLUT orthologs and their function and expression in mammals and birds, with emphasis on chickens and humans.
ARTICLE | doi:10.20944/preprints202310.0986.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: fermented sausage; lactic acid bacteria; food quality; phylogenetic analysis
Online: 16 October 2023 (16:51:50 CEST)
Alheira is a naturally fermented meat sausage traditionally made in the Portuguese region of Trás-os-Montes. Lactic Acid Bacteria (LAB) have been found to be the dominant microorganisms in alheira. This study aimed: 1) to characterize technological features and in vitro antimicrobial activity of LAB isolates; and 2) to reveal associations between such phenotypic characteristics and the isolates genotypically identified to species level through amplification and sequencing of the 16S ribosomal gene. Sixty-two LAB isolates were identified and Enterococcus faecium was the most prevalent (32.3%), followed by Leuconostoc mesenteroides (19.4%) and Latilactobacillus sakei (17.7%), aligning with previous research on traditional Portuguese fermented meat sausages. The phenotypic analysis of LAB isolates indicated diverse acidification capacities, proteolytic activities, and inhibitory effects against foodborne pathogens. Comprising the technological attributes, L. paracasei and L. mesenteroides had higher proteolytic activity (3.46 and 3.43 mm), whereas E. faecium and L. paracasei stood out for their acidifying capacity, with mean pH after 6 h of 5.78 and 6.03, respectively. Overall, lactobacilli presented higher inhibition diameter against the pathogens Staphylococcus aureus, Listeria monocytogenes and Salmonella Typhimurium. Although the mechanisms for inhibition of pathogen growth needs to be further elucidated, these findings enhance our understanding of LAB diversity and functionality in alheira sausages, contributing to product safety and quality assessment.
ARTICLE | doi:10.20944/preprints202309.1163.v1
Subject: Biology And Life Sciences, Virology Keywords: viral metagenomics; black-necked crane; genomic structure; phylogenetic analysis
Online: 18 September 2023 (11:52:56 CEST)
The black-necked crane is the only species that lives in the plateau. At present, there is little re-search on viral diseases of the black-necked crane. In this study, a virus metagenomics approach was employed to investigate the viral composition of black-necked cranes in Saga County, Shi-gatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly in-clude Genomoviridae, Parvoviridae, and Picornaviridae. Among them, one picornavirus genome is characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvoviruses genome were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomoviruses ge-nome were also acquired and identified as members of three different species including Ge-mykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable in-formation for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet and for monitoring, preventing, and treating black-necked cranes viral diseases.
ARTICLE | doi:10.20944/preprints202301.0114.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Leymus chinensis; fungal endophyte; stromata; morphological properties; phylogenetic properties
Online: 6 January 2023 (04:34:04 CET)
During Sep. 2011, forty-four Leymus chinensis culms with stroma development were collected from Inner Mongolia. Stromata surrounded the flag leaf sheathes, white, at the final stage of development. Perithecium but not asci were observed under microscope. Nine epichloid endophyte strains were obtained from Tongliao subdivision, and sixteen from Horqin. Morphological and phylogenetic properties of these strains were investigated. Morphological properties of these strains were similar among these 27 strains. Colonies could grow to 28.5~41.1 mm/21d at 25℃; phialides 24.1~26.4 μm long, 2.1~2.5 μm at base, tapering to less than 1.0 μm at tip; conidia reniform to elliptical, 4.7~5.5×2.8~3.5 μm, indicating typical properties of Epichloë endophytes. Based on the sequences of tefA and tubB gene fragments, strains isolated from Inner Mongolia formed a distinct subclade in E. bromolica/ E. yangzii clade, with a bootstrap value of 66% and 64% respectively. Considering morphological and phylogenetic properties, we tend to determine strains isolated from Leymus chinensis as a new taxon. The detailed taxonomic position of this taxon needs further investigations on hybridization or genomic sequence.
ARTICLE | doi:10.20944/preprints202007.0749.v1
Subject: Biology And Life Sciences, Virology Keywords: Bovine coronavirus; intersititial pneumonia; phylogenetic analysis; Real time PCR
Online: 31 July 2020 (13:46:21 CEST)
An outbreak of winter disease, complicated by severe respiratory syndrome, occurred in January 2020 in a high production dairy cow herd located in a hilly area of the Calabria region. Of the 52 animals belonging to the farm, 5 (9.6%) died with severe respiratory distress, death occurring 3-4 days after the appearance of the respiratory signs (caught and gasping breath). Microbiological analysis revealed absence of pathogenic bacteria whilst Real-time PCR identified the presence of RNA from Bovine Coronavirus (BCoV) in several organs: lungs, small intestine (jejunum), mediastinal lymph nodes, liver and placenta. Since being the only pathogen identified, BCoV was hypothesized to be the cause of the lethal pulmonary infection. Like the other CoVs, BCoV is able to cause different syndromes. Its role in calfhood diarrhoea and in mild respiratory disease is well known: we report instead the involvement of this virus in a severe and fatal respiratory disorder, with symptoms and disease evolution resembling that of Severe Acute Respiratory Syndromes (SARS).
ARTICLE | doi:10.20944/preprints201809.0566.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Montiaceae; life history; climate niche; polyploidy; phylogenetic comparative analysis (PhCA); natural selection (NS); natural drift (ND); chaos; stochasticity; determinism; principle of evolutionary idiosyncraticity (PEI)
Online: 2 October 2018 (12:06:57 CEST)
The present paper reviews evidence for ecological evolution of Montiaceae. Montiaceae (Portulacineae) comprise a family of ca. 275 species and ca. 25 subspecific taxa of flowering plants distributed mainly in extreme western America, with additional endemism elsewhere, including other continents and islands. They have diversified repeatedly across steep ecological gradients. Based on narrative analysis, I argue that phylogenetic transitions from annual to perennial life history have been more frequent than suggested by computational phylogenetic reconstructions. I suggest that a reported phylogenetic correlation between the evolution of life history and temperature niche is coincidental and not causal. I demonstrate how statistical phylogenetic comparative analysis (PhCA) missed evidence for marked moisture niche diversification among Montiaceae. I discount PhCA evidence for the relation between Montiaceae genome duplication and ecological diversification. Based on the present analysis of Montiaceae evolution, I criticize the premise of the prevalent statistical approach to PhCA, which tests Darwinian deterministic hypotheses against stochastic evolutionary null models. I discuss theoretical/empirical evidence that evolution is neither stochastic, nor Darwinistically-determined, but idiosyncratic. Idiosyncraticity describes the outcome of a stochastically perturbed nonlinear chaos-like process. The Principle of Evolutionary Idiosyncraticity (PEI) is based on the evolutionary theory of Natural Drift, which maintains that determinism in evolution is a property of the organism and not, as maintained by the theory of Natural Selection, its traits or its milieu. This determinism is characteristic of chaotic functions, which are absolutely determinate, generate self-similarity, but remain absolutely unpredictable. PEI explains precisely observations that evolution proceeds not linearly, but chaotically, producing both quasi-linear fractal-like patterns and non-linear jumps. PEI has ramifications for all areas of macroevolutionary research. In particular, it demonstrates both the fallacy and futility of the statistical PhCA approach that interprets evolutionary causes in terms of evolutionary correlations. However, statistical methods of PhCA can be applied heuristically and fruitfully to reveal idiosyncraticity and discover evolutionary novelty. This, in turn, is demonstrated by the emergence of statistical anomalies in evolutionary analyses of Montiaceae.
ARTICLE | doi:10.20944/preprints202304.0236.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Fowl adenovirus; phylogenetic; hydropericardium hepatitis syndrome; gross lesions; Chickens; Azerbaijan
Online: 12 April 2023 (04:00:51 CEST)
Hydropericardium hepatitis syndrome (HHS) caused by fowl adenovirus-4 have been frequently reported in commercial chickens from several countries causing significant economical losses. In Azerbaijan, fowl adenovirus infections in broiler and layer breeders flocks cause severe disease and mortality. Here we investigated the pathological lesions and the dissemination of fowl adenovirus-4 into the visceral organs of infected birds. Tissue samples containing liver, heart and spleen from 20 necropsied chickens were collected on the FTA cards and presence of fowl adenovirus was analysed by PCR and sequencing. Postmortem findings of both broiler and layer breeder chickens were similar, and the most affected organs were the liver with hepatitis and the heart with hydropericardium lesions. Other postmortem signs include swollen kidneys with haemorrhages and small white foci on the surface of the spleens. In some birds intestinal congestion and ecchymotic hemorrhages were also apparent. The PCR analysis revealed that all collected organs from 20 birds showed presence of fowl adenovirus-4 genome. The sequence analysis showed that fowl adenovirus-4 prevalent in Azerbaijan carry more closer phylogenetic relationship with the viruses prevalent in the Middle East, Far East and Indian subcontinent. However, a distinct diversity was seen from the strains prevalent in Europe, North and South America. This study will provide evidence the impact of fowl adenovirus-4 on the poultry production and improved preventive disease control strategies are required to reduce the HHS disease in chickens in Azerbaijan.
ARTICLE | doi:10.20944/preprints202108.0340.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Escherichia coli; Antimicrobial resistance; Food samples; Phylogenetic group; Genetic diversity
Online: 16 August 2021 (13:35:58 CEST)
The emergence of multi-drug resistant E. coli is an important matter of increasing considerable concern to global public health. The aim of this study was to investigate the incidence, antibiotic resistance pattern, phylogroups and genetic variation of E. coli isolates from raw milk, vegetable salad and ground meat samples. Methods: Culture-based techniques, Kirby-Bauer disk diffusion susceptibility testing, PCR and RAPD assays were used to determine the incidence rate, antimicrobial resistance pattern, phylogenetic groups and genetic diversity of the E. coli isolates. Results: E. coli isolates were highly resistant to amoxicillin (79.16%), trime-thoprim-sulfamethoxazole (70.83%), amoxicillin-clavulanic acid (62.50%), tetracycline (54.16%), chloramphenicol (54.16%), nitrofurantoin (54.16%), ampicillin (45.83%), streptomycin (45.83%), and kanamycin (33.33%); and completely susceptible to norfloxacin and azithromycin. 70.83% of the isolates were multi-drug resistant. Most E. coli isolates (46%) belonged to phylogroup A. RAPD with UBC245 primer categorized the isolates into 11 clusters. A high level of genetic di-versity was found among the isolates; however, 33.3% of the isolates were grouped in a major cluster (R5). Conclusions: Antibiotic resistance patterns are randomly distributed among the ge-netic clusters. Novel, practical, efficient food safety control and surveillance systems of multi-drug resistant foodborne pathogens are required to control the foodborne pathogen contamina-tion.
ARTICLE | doi:10.20944/preprints201608.0040.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: seeds; ELISA; Fusarium; morphological data analysis; mycotoxins; phylogenetic analysis S
Online: 4 August 2016 (10:12:54 CEST)
Adlay seed samples were collected from 3 adlay growing regions (Yeoncheon, Jeonnam and Eumseong regions) in Korea during 2012. Among all the samples collected, 400 seeds were tested for fungal occurrence by standard blotter and test tube agar methods and different taxonomic groups of fungal genera were detected. The most predominant fungal genera encountered were Fusarium, Phoma, Alternaria, Cladosporium, Curvularia, Cochliobolus and Leptosphaerulina. The occurrence of Fusarium species were 45.6% and based on the combined sequences of two protein coding genes, EF-1a, Beta-tubulin and phylogenetic analysis, 10 species were characterized as F. incarnatum (11.67%), F. kyushense (10.33%), F. fujikuroi (8.67%), F. concentricum (6.00%), F. asiaticum (5.67%), F. graminearum (1.67%), F. miscanthi (0.67%), F. polyphialidiom (0.33%), F. armeniacum (0.33%) and F. thapsinum (0.33%). The ability of these isolates to produce mycotoxins fumonisin (FUM) and zeralenone (ZEN) were tested by ELISA quantitative analysis method. The result revealed that fumonisin (FUM) was produced only by F. fujikuroi and zeralenone (ZEN) by F. asiaticum & F. graminearum. Mycotoxigenic species were then examined for their morphological characteristics to confirm their identity. Morphological observations of the species correlated well with their molecular identification and confirmed as F. asiaticum, F. fujikuroi and F. graminearum.
ARTICLE | doi:10.20944/preprints201901.0212.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: DHAV-1; DHAV-3; Phylogenetic analysis; One-tube RT-PCR; Simultaneously
Online: 22 January 2019 (11:08:19 CET)
The co-circulation of duck hepatitis A virus subtypes 1 (DHAV-1) and 3 (DHAV-3) in ducklings has resulted in significant economic losses. Because ducklings infected with DHAV-1 or DHAV-3 show similar clinical signs and gross lesions, it is important to discriminate these subtypes as early as possible for better clinical management. On the basis of multiple alignments of the 5′-noncoding region sequences of strains DHAV-1 and DHAV-3, universal and type-specific primers were designed and synthesized. Using the primers in a one-tube reverse transcription-PCR (RT-PCR) assay, reference strains of DHAV-1 and DHAV-3 (isolated over a span of 60 years and covering many different countries) were successfully amplified, indicating that the primer sequences were completely conserved. The amplicon sequences results and the sizes of amplicons from reference DHAV-1 and DHAV-3 isolates correlated completely with their genotypes. Moreover, with this one-tube RT-PCR system, the amplicon sizes of liver samples of reference DHAV-1- or DHAV-3-infected birds matched perfectly with their respective genotypes, as determined by virus isolation and neutralization tests. No other RNA viruses of duck origin were detected with the synthesized primers. The sensitivity of viral RNA detection was 10 pg. With this system, 20% genotype 1, 45% genotype 3, and 9% co-infection of the two genotypes were detected in 55 clinical samples. This novel approach could be used for the rapid genotyping DHAV-1 and/or DHAV-3 infection in routine clinical surveillance or epidemiologic screening.
ARTICLE | doi:10.20944/preprints201805.0169.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: cyanobacteria; cyanotoxins; nutrient enrichment; akinetes; harmful algal blooms; PCR; phylogenetic analyses
Online: 10 May 2018 (15:37:51 CEST)
The presence of harmful algal blooms (HABs) and cyanotoxins in drinking water sources poses a great threat to human health. The current study employed molecular techniques to determine the occurrence of non-toxic and toxic cyanobacteria species in the Limpopo River basin based on the phylogenetic analyses of 16S rRNA gene. The bottom sediments samples were collected from selected rivers: Limpopo, Crocodile, Mokolo, Mogalakwena, Nzhelele, Lephalale, Sand Rivers (South Africa); Notwane (Botswana), Shashe River and Mzingwane River (Zimbabwe). The physical-chemical analysis of the bottom sediments showed the availability of nutrients, nitrates and phosphates, in excess of 0.5 mg/l for most of river sediments, alkaline pH and salinity in excess of 500 mg/l. The FlowCam showed the dominant cyanobacteria species identified from the samples were Microcystis species, followed by Cylindrospermopsis raciborskii, Phormidium and Planktothrix species and this was confirmed by molecular techniques. Nevertheless, two samples showed the amplification of cylindrospermopsin polyketide synthetase gene (S3 and S9) while two samples showed amplification for microcystin/nodularin synthetase gene (S8 and S13). Thus these findings may imply the presence of toxic cyanobacteria species in the river sediments. The presence of cyanobacteria may be hazardous to human because rural communities and farmers who abstract water from Limpopo river catchment for human consumption, livestock and wildlife watering and irrigation.
ARTICLE | doi:10.20944/preprints201907.0013.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Rett Syndrome; intrinsically disordered region; phylogenetic profile analysis; post-transcriptional modification; methyl-CpG-binding protein 2; cyclin-dependent kinase-like 5; forkhead box protein G1
Online: 1 July 2019 (11:59:56 CEST)
Rett syndrome (RTT) is mainly caused by mutations in methyl CpG-binding protein 2, cyclin-dependent kinase-like 5, or forkhead box protein G1. These RTT-causing proteins harbor an intrinsically disordered region (IDR) whose conformation exhibits spatiotemporal heterogeneity, which not only confer versatility to the protein, but also implicates them in diseases. The IDR generally evolves more rapidly than an ordered structure. In this study, we examined the relationship between pathogenic RTT-associated point mutations in RTT-causing proteins and the evolutionary dynamics of sequence features including structural order–disorder, phosphorylation sites, and evolutionary rates. We also analyzed the molecular properties and evolution of proteins that interact with RTT-causing proteins in terms of phylogenetic profiles, tissue specificity, subcellular localization, expression level, and functions. The results indicate that constrained IDRs may function by forming contacts with other regions in the protein sequence causing pathogenic missense mutations likely to arise in the rapidly evolving IDR and affect molecular networks, leading to disease. The results also provide novel insights into the genetic basis for RTT and the evolution of the neocortex in higher vertebrates.
ARTICLE | doi:10.20944/preprints202308.0123.v1
Subject: Biology And Life Sciences, Other Keywords: Entropy; Electron-Ion Interaction Potential; COVID-19; Phylogenetic analysis; SARS-CoV-2
Online: 2 August 2023 (03:29:01 CEST)
The SARS-CoV-2 virus, causative agent of COVID-19, is known for its genetic diversity. Virus variants of concern (VOCs) as well as variants of interest (VOIs) are classified by the World Health Organization (WHO) according to their potential risk to global health. This study seeks to enhance the identification and classification of such variants by developing a novel bioinformatics criterion centered on the virus's spike protein (SP1), a key player in host cell entry, immune response, and a mutational hotspot. To achieve this, we pioneered a unique phylogenetic algorithm which calculates EIIP-entropy as a distance measure based on the distribution of the Electron-Ion Interaction Potential (EIIP) of amino acids in SP1. This method offers a comprehensive, scalable, and rapid approach to analyze large genomic data sets and predict the impact of specific mutations. This innovative approach provides a robust tool for classifying emergent SARS-CoV-2 variants into potential VOCs or VOIs. It could significantly augment surveillance efforts and understanding of variant characteristics, while also offering potential applicability to the analysis and classification of other emerging viral pathogens and enhancing global readiness against emerging and re-emerging viral pathogens.
ARTICLE | doi:10.20944/preprints202306.1711.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: florescence in situ hybridization; Jatropha curcas; phylogenetic tree analysis; Ty1-copia retrotransposons
Online: 25 June 2023 (04:52:06 CEST)
Jatropha curcas is a potential energy crop and has been identified as a significant resource for biodiesel. Retrotransposons occupy the plant genome in a large proportion, so the specific retrotransposon characterization will help improve understanding of the Jatropha genome evolution and organization. This research aimed to characterize and classify Ty1-copia retrotransposons in J. curcas using specific gene sequence and to detect the distribution of Ty1-copia in J. curcas and J. integerrima chromosomes using florescence in situ hybridization (FISH) method. Ty1-copia sequences from J. curcas were isolated using three degenerate primer sets specific to the conserved Ty1-copia reverse transcriptase gene for polymerase chain reaction (PCR). FISH technique using the Ty1-copia probes was used to map physically on J. curcas and J. integerrima chromosomes. Altogether, 164 Ty1-copia sequences were obtained to use for the phylogenetic analysis and were classified into the four families of TAR, Angela, Ale and Bianca. Physical map using FISH method of Angela and Ale families on J. curcas and J. integerrima chromosomes exhibited biases for specific regions around the centromeres or at the chromosome terminal regions. The study indicates the high variation of the Ty1-copia elements in the genome of Jatropha. These results will enhance understanding of retrotransposon chromosomal distribution and evolution of the J. curcas genome and also promotion of retrotransposon possible utilization in J. curcas improvement projects using retrotransposon-based markers.
REVIEW | doi:10.20944/preprints202110.0258.v2
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: phylogeny estimation; multiple sequence alignment; phylogenetic placement; phylogenomics; taxon identification; maximum likelihood
Online: 12 January 2022 (18:56:42 CET)
With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the last few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g., incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements.
REVIEW | doi:10.20944/preprints202004.0382.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: COVID-19; ACE2; SARS-CoV; neurological disorders; phylogenetic perspective; coronavirus; CNS; PNS
Online: 21 April 2020 (08:30:59 CEST)
After the emergence of Severe Acute Respiratory Syndrome Coronavirus(SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in the last two decades, the world is facing its new challenge in SARS-CoV-2 pandemic with unfathomable global responses. The characteristic clinical symptoms for Coronavirus (COVID-19) affected patients are high fever, dry-cough, dyspnoea, lethal pneumonia whereas some patients also show few additional neurological signs such as headache, nausea, vomiting. The accumulative evidences suggest that Coronavirus is not only confined within the respiratory tract and that may also invade in central nervous system (CNS), peripheral nervous system (PNS) inducing some fatal Neurological diseases. Here we analyse the phylogenetic perspective of SARS-CoV2 with other strains of β-Coronaviridae from a standpoint of neurological spectrum disorders. Based on the existing case reports, literature and open data-bases, we also analyse the differential distribution of neurological impairments in COVID-19 positive patients along with angiotensin-converting enzyme-2(ACE2) expression dynamics in neuronal and non-neuronal tissue of central and peripheral nervous system. Besides, we discuss the need for modulations in clinical approach from a neurological point of view, as a measure towards reducing disease transmission, morbidity and mortality in SARS-CoV2 positive patients.
ARTICLE | doi:10.20944/preprints201902.0018.v2
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: temperate forests; species richness; lineage diversity; phylogenetic diversity; United States; trees; TILD
Online: 13 February 2019 (10:15:50 CET)
Lineage diversity can refer to the number of genetic lineages within species or to the number of deeper evolutionary lineages, such as genera or families, within a community. Community lineage diversity (CLD) is of interest to ecologists, evolutionary biologists, biogeographers, and those setting conservation priorities. Despite its relevance, it is not clear how to best quantify CLD. With North American tree communities as an example, we test which taxonomic and phylogenetic metrics best measure CLD. We find that phylogenetic metrics outperform taxonomic metrics. Faith’s phylogenetic diversity performs well, but is skewed towards the number of lineages in recent time. The best metric is newly derived here, and termed time integrated lineage diversity (TILD). Mapping the lineage diversity of tree communities across the contiguous United States, we find a spatial pattern differing from that of species richness in key areas. The Pacific Northwest, Great Lakes Region, state of Maine, and south-eastern piedmont and coastal plain forests all emerge as areas high in lineage diversity, but relatively lower in species richness. We urge the consideration of lineage diversity, as well as species richness, when setting conservation priorities.
ARTICLE | doi:10.20944/preprints202311.1514.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Fusarium spp.; genetic diversity; pathogenicity; phylogenetic analyses; resistance; root rot; Sanger sequencing; soybean
Online: 23 November 2023 (11:06:49 CET)
Fusarium spp. are commonly associated with the root rot complex of soybean (Glycine max). Previous surveys identified six common Fusarium species from Manitoba, including F. oxysporum, F. redolens, F. graminearum, F. solani, F. avenaceum and F. acuminatum. This study aimed to determine their pathogenicity, assess host resistance and evaluate the genetic diversity of Fusarium spp. isolated from Canada. Pathogenicity was tested on two cultivars, ‘Akras’ (moderate resistance) and ‘B150Y1’ (susceptible), under greenhouse conditions. The virulence of the fungal isolates varied, with root rot severities ranging from 1.5 to 3.3 on a 0-4 scale. The six species were used to screen a panel of 20 Canadian soybean cultivars for resistance in a greenhouse. Cluster and principal component analyses were conducted based on the same traits as for the pathogenicity study. Two of the cultivars, ‘P15T46R2’ and ‘B150Y1’, were consistently found to be tolerant to F. oxysporum, F. redolens, F. graminearum and F. solani. To investigate the incidence and prevalence of Fusarium spp. in Canada, fungi were isolated from 106 soybean fields surveyed across Manitoba, Saskatchewan, Ontario and Quebec. Two-hundred twenty-one Fusarium isolates were identified, with phylogenetic analyses indicating diversity of the isolates in the major soybean production regions of Canada.
REVIEW | doi:10.20944/preprints202309.0495.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: phylogenomics; synteny; chromosomes; long-read sequencing; tree of life; orthology; phylogenetic trees; incongruence
Online: 7 September 2023 (07:21:52 CEST)
Reconstructing the Tree of Life remains a central goal in biology. Early methodologies, relying on comparative anatomy or alignments of small numbers of genetic loci, often yielded conflicting evolutionary histories, undermining confidence in the results. Investigations based on phylogenomics, which uses hundreds to thousands of loci for phylogenetic inquiry, often provide a clearer picture of life's history, but certain branches have remained challenging to resolve. Particularly problematic nodes include the root of the animal tree and the relationships among major clades of teleost fish, a group encompassing nearly half of all vertebrates. To address these debates, recent studies tested the utility of an emerging phylogenomic marker: synteny, the conserved collinearity of orthologous loci in two or more organisms. Synteny exhibits compelling phylogenomic potential, while also raising new challenges. We discuss the history of phylogenetics, contentious branches in the Tree of Life, and the use of synteny to address them. We propose five research questions to help guide the use of synteny data in phylogenomic studies. Synteny-based analyses of highly contiguous genome assemblies mark a new chapter in the phylogenomic era and the quest to reconstruct the Tree of Life.
ARTICLE | doi:10.20944/preprints202212.0232.v1
Subject: Biology And Life Sciences, Virology Keywords: coronavirus; genome; recombination; COVID-19; reservoir host; secondary host; phylogenetic support; tree reconstruction
Online: 13 December 2022 (07:44:48 CET)
Phylogenetic trees of coronaviruses are difficult to interpret because they undergo frequent ge-nomic recombination. Here, we propose a new method, named coloured genomic bootstrap (CGB) barcodes, to highlight the polyphyletic origins of human sarbecoviruses and understand their host and geographic ori-gins. The results indicate that SARS-CoV and SARS-CoV-2 contain genomic regions of mixed an-cestry originating from horseshoe bat (Rhinolophus) viruses. First, different regions of SARS-CoV share exclusive ancestry with five Rhinolophus viruses from Southwest China (RfYNLF/31C: 17.9%; RpF46: 3.3%; RspSC2018: 2.0%; Rpe3: 1.3%; RaLYRa11: 1.0%) and 97% of its genome can be related to bat viruses from Yunnan (China), supporting its emergence in Rhinolophus species of this province. Second, different regions of SARS-Cov-2 share exclusive ancestry with eight Rhi-nolophus viruses from Yunnan (RpYN06: 5.8%; RaTG13: 4.8%; RmYN02: 3.8%), Laos (RpBA-NAL103: 3.3%; RmarBANAL236: 1.7%; RmBANAL52: 1.0%; RmBANAL247: 0.7%), and Cam-bodia (RshSTT200: 2.3%), and 98% of its genome can be related to bat viruses from northern Laos and Yunnan, supporting its emergence in Rhinolophus species of this region. Although CGB barcodes are very useful to retrace the origins of human sarbecoviruses, further investigations are needed to better apprehend the diversity of coronaviruses in bats from Cambo-dia, Laos, Myanmar, Thailand and Vietnam.
Subject: Biology And Life Sciences, Virology Keywords: origin of viruses; phylogenetic reconstruction; reductive evolution; obligate intracellular parasites; Varidnaviria; Bamfordvirae; Nucleocytoviricota
Online: 19 September 2020 (03:51:15 CEST)
The extension of virology beyond its traditional medical, veterinary or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on earth. In particular, virus isolation studies involving unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure and morphology, genome size and gene content, or mode of replication. Complemented by large-scale metagenomic analyzes, these discoveries have rekindled interest in the enigma of the evolutionary origin of viruses, for which no simple definition encompassing all of their diversity is still unanimous. Several laboratories have repeatedly tackled the deep reconstruction of the evolutionary history of viruses, using various methods of molecular phylogeny applied to the few shared genes detected in certain virus groups (e.g. the Nucleocytoviricota). Beyond the practical difficulties of establishing reliable homology relationships from extremely divergent sequences, I present here purely conceptual arguments highlighting several fundamental limitations plaguing the reconstruction of the deep evolutionary history of viruses, and even more the identification of their unique of multiple origin (s). Those limitations are direct consequences of the particularly random mechanisms which govern the reductive evolution of obligate intracellular parasites.
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: nucleoid-associated proteins (NAPs); moonlighting proteins; drug target; biofilm; specificity determination; phylogenetic analysis
Online: 7 June 2020 (09:07:56 CEST)
Nucleoid-associated proteins (NAPs) play an architectural role by bending, bridging, and wrapping the DNA along with a regulatory role of controlling various transcriptional units in the cell. Previews reviews have highlighted the role of HU and its paralog IHF plays in intracellular function as a transcriptional regulator, nucleoid bending protein and sometimes also moonlights in other functions. This review highlights along with the canonical functions of HU and IHF which affects genes responsible for translational machineries, cell wall biosynthesis, aerobic respiration and virulence ; other non-canonical roles which HU plays outside the cellular milieu, notably in acting as an adhesin and playing role in host-cell adhesion, its role in biofilm architecture and its association with cationic low complexity region, resembling histone like H1 proteins. HU and IHF thus has evolved as a hub protein performing a vast type of functions which makes it a important drug target for antibacterial therapy.
BRIEF REPORT | doi:10.20944/preprints202003.0091.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; coronavirus; angiotensin converting enzyme 2 (ACE2); receptor utilization; phylogenetic analysis.
Online: 5 March 2020 (12:12:38 CET)
SARS-CoV-2, the newly identified human coronavirus causing severe pneumonia epidemic, was probably originated from Chinese horseshoe bats. However, direct transmission of the virus from bats to humans is unlikely due to lack of direct contact, implying the existence of unknown intermediate hosts. Angiotensin converting enzyme 2 (ACE2) is the receptor of SARS-CoV-2, but only ACE2s of certain species can be utilized by SARS-CoV-2. Here, we evaluated and ranked the receptor-utilizing capability of ACE2s from various species by phylogenetic clustering and sequence alignment with the currently known ACE2s utilized by SARS-CoV-2, predicting potential intermediate hosts of SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202311.0621.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: enteric virus; picobirnavirus; brazilian animals; page, rt-pcr; rdrp gene; phylogenetic analysis; genogroup I
Online: 9 November 2023 (11:24:00 CET)
This study aimed to detect picobirnavirus (PBV) in the fecal samples of wild and domestic animals from 2014 to 2016 in the Amazon biome. Fecal samples from different animals, including birds (n=41) and mammals (n=217) were used. The PAGE test showed negativity for PBV. However, 32 samples (12.4%, 32/258) showed positive results in RT-PCR analyses. Among the positive sam-ples, pigs and cats, both with 28.12% (9/32), registered the highest frequencies. In phylogenetic analysis, eight sequences from positive samples grouped in the Genogroup 1 of PBV (PBV GI). PBV occurrence was significantly related to cats and pigs, but not other mammals or birds, in-dependently of their geographical origin. Nucleotide analysis demonstrated similarity among the feline group, but the absence of a defined structure between the clades. PBVs are highly wide-spread viruses that can affect the most diverse types of hosts in the Amazon biome, including humans.
REVIEW | doi:10.20944/preprints202210.0313.v1
Subject: Biology And Life Sciences, Virology Keywords: diagnosis; distribution; emaraviruses; forest trees; Fimoviridae; genome organization; phylogenetic relations; protein domains; symptomatology; transmission
Online: 20 October 2022 (14:09:37 CEST)
: Emaravirus (Order Bunyavirales; Family Fimoviridae) is a genus comprising over 20 emerging plant viruses with a worldwide distribution and economic impact. Emaraviruses infect a variety of host plants and have especially become prevalent in important long-living woody plants. These viruses are enveloped, with a segmented, single-stranded, negative-sense RNA genome and are transmitted by eriophyid mites or mechanical transmission. Emaraviruses have four core genome segments encoding an RNA-dependent RNA polymerase, a glycoprotein precursor, a nucleocapsid protein, and a movement protein. They also have additional genome segments, whose number varies widely. We report here that the proteins encoded by these segments form three main homology groups: a homolog of the sadwavirus Glu2 Pro glutamic protease; a protein involved in pathogenicity, which we named “ABC”; and a protein of unknown function, which we named “P55”. The distribution of these proteins parallels the emaravirus phylogeny and suggests, with other analyses, that emaraviruses should be split into at least two genera. Reliable diagnosis systems are urgently needed to detect emaraviruses, assess their economic and ecological importance, and take appropriate measures to prevent their spread (such as routine testing, hygiene measures, and control of mite vectors). Additional research needs include understanding the function of emaravirus proteins, breeding resistant plants and clarifying transmission modes.
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Magnesium transporter; Comparative analysis; Malvaceae; Theobroma, Gossypium; Corchorus; Expression analysis; Gene structure; Phylogenetic analysis.
Online: 27 July 2021 (22:49:36 CEST)
Magnesium (Mg) is a vital element, which involves in various key cellular processes in plants. Mg transporter (MGT) genes play an important role in magnesium distribution and ionic balance maintenance. Here, MGT family members were identified and characterized in three species of the plant family Malvaceae, including Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum to improve our understanding of their structure, regulatory systems, functions, and possible interactions. We identified 18, 41, and 16 putative non-redundant MGT genes from the genome of T. cacao, G. hirsutum, and C. capsularis, respectively, which were clustered into five groups within maximum likelihood tree. Several segmental/tandem duplication events were determined between MGTs genes. It seems that MGTs were slowly evolving and have been evolved under a purifying selection. Analysis of gene promoter regions showed that MGTs have a high potential to respond to biotic/abiotic stresses as well as hormones. The expression patterns of MGT genes revealed their possible T. cacaorole in response to P. megakarya fungi in T. cacao, whereas MGT genes showed differential expression in various tissues and respond to several abiotic stresses, including cold, salt, drought, and heat stress in G. hirsutum. Besides, the co-expressions network of MGTs indicated that genes involved in auxin responsive, lipid metabolism, cell wall organization, and photoprotection can interact with MGTs.
Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: l. monocytogenes; humans; animals; food; antimicrobial and virulence genes; bioinformatic analysis; prfA phylogenetic analysis
Online: 17 November 2019 (09:48:54 CET)
Serious outbreaks of foodborne disease have been caused by Listeria monocytogenes found in retail delicatessens and the severity of disease is significant, with high hospitalization and mortality rates. Little is understood about the formidable public health threat of L. monocytogenesin all four niches, humans, animals, food and environment in Egypt. This study analyzed the presence of L. monocytogenes collected from the four environmental niches and bioinformatic analysis was implemented to analyze and compare the data. PCR was used to detect virulence genes encoded by pathogenicity island (LIPI-1). prfA amino acid substation that causes constitutive expression of virulence was common in 77.7% of isolates. BLAST analysis did not match other isolates in the NCBI database suggesting this may be a characteristic of the region associated with these isolates. A second group included the NH1 isolate originating in China, and BLAST analysis showed this prfA allele was shared with isolates from other global locations such as Europe and North America. Identification of possible links and transmission pathways between the four niches, helps to decrease the risk of disease in humans, to take more specific control measures in the context of disease prevention, to limit economic losses associated with food recalls and highlightens the need to treatment options.
ARTICLE | doi:10.20944/preprints202011.0065.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Carbapenem resistant Enterobacteriaceae (CRE); E.coli; Antimicrobial Resistance; Multidrug resistance; Phylogenetic diversity; chicken; food animals; Antimicrobials
Online: 2 November 2020 (17:14:31 CET)
Carbapenem resistant Enterobacteriaceae (CRE) has been public health risk in several countries and recent reports indicate the emergence of CRE in food animals. This study was conducted to investigate the occurrence, resistance patterns, and phylogenetic diversity of CRE E.coli from chicken. Routine bacteriology, PCR detection of E.coli species, multiplex PCR to detect carbapenemase encoding genes and phylogeny of CRE E. coli were conducted. The results show that 24.36 % (19/78) were identified as CRE based on the phenotypic identifications of which 17 were positive for the tested carabanemase genes. The majority, 57.99% (11/19) of the isolates harbored multiple carbapenemase genes. Four isolates harbored all blaNDM blaOXA, blaIMP, five and two different isolates harbored blaNDM and blaOXA, and blaOXA and blaIMP respectively. The Meropenem, Imipenem and Ertapenem MIC values for the isolates ranged from 2g/mL to ≥256g/mL. Phylogenetic grouping showed that the CRE E.coli isolates belonged to five different groups; groups A, B1, C, D and unknown. The detection of carbapenem resistant E.coli in this study shows that CRE is has become an emerging problem in farm animals, particularly, in poultry farms. This also implies the potential public health risks posed by CRE from chicken to the consumers.
REVIEW | doi:10.20944/preprints202309.0905.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: phylogenetics; hybridization; introgression; horizontal gene transfer; lateral gene transfer; phylogenetic incongruence; gene-tree-species-tree discordance
Online: 14 September 2023 (04:50:27 CEST)
Phylogenomics has enriched our understanding of the Tree of Life. Non-vertical modes of evolution—such as hybridization/introgression and horizontal gene transfer—deviate from a strictly bifurcating tree model, mirroring a network-like or reticulate structure. Here, we present an overview of a phylogenomic workflow for inferring organismal histories, calibrating those histories to evolutionary time, and detecting reticulate evolution. Mitigating analytical sources of error facilitates accurate reconstructions of evolutionary history and, in turn, characterization of non-vertical modes of evolution. Workflows and methods discussed herein may aid in the rigorous inference of organismal histories in geologic time and reticulation, providing a clearer understanding of the evolutionary process.
ARTICLE | doi:10.20944/preprints202308.1317.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: AF2-CF modeling; LeuT fold; Slc11 synapomorphy; carrier conformation switch; phylogenetic analysis; in silico mutagenesis; epistasis
Online: 18 August 2023 (08:16:19 CEST)
Transmembrane carriers of the Slc11 family catalyze proton (H+)-dependent uptake of divalent metal-ions (Me2+) such as manganese and iron - vital elements coveted during infection. Slc11 mechanism of high affinity Me2+ cell import is selective and conserved between prokaryotic (MntH) and eukaryotic (Nramp) homologs, though processes coupling the use of the proton motive force to Me2+ uptake evolved repeatedly. Adding bacterial piracy of Nramp genes spread in distinct environmental niches suggests selective gain of function that may benefit opportunistic pathogens. To better understand Slc11 evolution Alphafold (AF2)/Colabfold (CF) 3D predictions for bacterial sequences from sister clades of eukaryotic descent (MCb and MCg) were compared using both native and mutant templates. AF2/CF model an array of native MCb intermediates spanning the transition from outward open (OO) to inward open (IO) carrier. In silico mutagenesis targeting i) a set of (evolutionary coupled) sites that may define Slc11 function (putative synapomorphy), and ii) residues from networked communities evolving during MCb transition, indicate Slc11 synapomorphy primarily instructs Me2+-selective conformation switch which unlocks carrier inner gate, and contributes to Me2+ binding site occlusion and outer gate locking. Inner gate opening apparently proceeds from interaction between transmembrane helix (h) h5, h8 and h1a. MCg1 xenologs revealed marked differences in carrier shape and plasticity, owing partly to altered intramolecular H+-network. Yet, targeting Slc11 synapomorphy also converted MCg1 IO models to OO state, apparently mobilizing the same residues to control gates. But MCg1 response to mutagenesis differed, extensive divergence within this clade correlating with MCb-like modeling properties. Notably, MCg1 divergent epistasis marks emergence of the genus Bordetella-Achromobacter. Slc11 synapomorphy localizes to the 3D areas that deviate least among MCb and MCg1 models (either IO or OO) implying it constitutes a 3D network of residues articulating Me2+-selective carrier conformation switch which is maintained in fast evolving clades at the cost of divergent epistatic interactions impacting carrier shape and dynamics.
ARTICLE | doi:10.20944/preprints202308.1579.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: highly pathogenic avian influenza A H5N8; clade 18.104.22.168b; Kosovo; domestic poultry; phylogenetic network analysis; viruses; persistent circulation
Online: 22 August 2023 (12:59:41 CEST)
In this study, we report the first outbreak of highly pathogenic avian influenza (HPAI) A H5N8, clade 22.214.171.124b in Kosovo on May 19, 2021. The outbreak consisted of three temporal phases: May–June 2021, September–November 2021, and January–May 2022. In total, 32 backyard and 10 commercial holdings tested positive for the virus, affecting 179,198 poultry. Interestingly, the third and last phase of the outbreak coincided with the massive H5N1 clade 126.96.36.199b epidemic in Europe. Phylogenetic analyses of 28 viral strains from Kosovo revealed that they were closely related to the H5N8 clade 188.8.131.52.b viruses that have been circulating in Albania, Bulgaria, Croatia, Hungary, and Russia in early 2021. Whole genome sequencing of the 25 and partial sequencing of 3 H5N8 viruses from Kosovo showed high nucleotide identity, forming a distinctive cluster and suggesting a single introduction. The results of the network analysis were in accordance with the three epidemic waves and suggested that the viral diffusion could have been caused by secondary spreads among farms and/or different introductions of the same virus from wild birds. The persistent circulation of the same virus over a one-year period highlights the potential risk of the virus becoming endemic, especially in settings with non-adequate biosecurity.
ARTICLE | doi:10.20944/preprints202208.0024.v1
Subject: Biology And Life Sciences, Virology Keywords: highly pathogenic avian influenza viruses; H5N8; H5N5; Clade 184.108.40.206; phylogenetic network analyses; next-generation sequencing; MinION; epidemiology
Online: 1 August 2022 (14:57:42 CEST)
During autumn/winter in 2016 – 2017 and 2020 – 2021, highly pathogenic avian influenza viruses (HPAIV) caused severe outbreaks in Germany and Europe. Multiple clade 220.127.116.11b H5 HPAI subtypes were responsible for increased mortality in wild birds and high mortality and massive losses in the poultry sector. To clarify putative entry sources and delineate interconnections between outbreaks in poultry holdings and wild birds, we applied whole-genome sequencing and phylodynamic analyses combined with the results of epidemiological outbreak investigations. Varying outbreak dynamics of the distinct reassortants allowed for the identification of individual, putatively wild bird-mediated entries into backyard holdings, several clusters comprising poultry holdings, local virus circulation for several weeks, direct farm-to-farm transmission and potential reassortment within a turkey holding with subsequent spill-over of the novel reassorted virus into the wild bird population. Whole-genome sequencing allowed for allowed for a unique high-resolution molecular epidemiology analysis of HPAIV H5Nx outbreaks, recommended to be used as a standard tool. The presented detailed account of the genetic, temporal and geographical characteristics of the recent German HPAI H5Nx situation emphasizes the role of poultry holdings as an important source of novel genetic variants and reassortants.
REVIEW | doi:10.20944/preprints202108.0058.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; Phylogenetic analysis; Next generation sequence analysis; Virus-Host interaction; Immunology; Antiviral agents; Vaccine; Virus diagnosis
Online: 2 August 2021 (16:17:24 CEST)
The global COVID-19 pandemic claiming global spread continues to evolve, now to the verge of a third wave of outbreak possibly caused by the novel variants of concern of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). The test positivity rate (TPR) and case fatal-ity rate (CFR) have increased steeply in the second wave of COVID-19 compared to the first. From the example of Kerala, a state in southern India, positivity increased from 1.33% at the peak of wave one in 10th June 2020 to 13.45% during 10th June 2021 in the second wave of pandemic. SARS-CoV-2 is an enveloped single-stranded RNA virus. Angiotensin-Converting Enzyme-2 (ACE-2) is a trans membrane surface protein present on multiple types of cells in the human body to which the viral spike protein attaches. Genetic variations in the SARS-CoV-2 and ACE2 receptor can affect the transmission, clinical manifestations, mortality and the efficacy of drugs and vaccines for COVID-19. Mutations are the primary cause of genetic variations. Given the high TPR and CFR, it is necessary to understand the variations of SARS-CoV-2 and cellular receptors of SARS-CoV-2 at the molecular level. In this review, we summarize the impact of genetic and ep-igenetic variations in determining COVID-19 pathogenesis and disease outcome.
ARTICLE | doi:10.20944/preprints201911.0061.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: rett syndrome; intrinsically disordered region; phylogenetic profile analysis; post-transcriptional modification; methyl-cpg-binding protein 2; cyclin-dependent kinase-like 5; forkhead box protein g1
Online: 6 November 2019 (10:58:54 CET)
Rett syndrome (RTT), a neurodevelopmental disorder, is mainly caused by mutations in methyl CpG-binding protein 2 (MECP2), which alter the functions of domains to either bind to methylated DNA or interact with a transcriptional co-repressor complex. It has been established that alterations in cyclin-dependent kinase-like 5 (CDKL5) or forkhead box protein G1 (FOXG1) correspond to distinct neurodevelopmental disorders, given that a series of studies have indicated that RTT is also caused by alterations in either one of these genes. We tried to elucidate RTT through evolution and structure assessment of MeCP2, CDKL5, and FOXG1, by focusing on their binding partners and disordered structures. Here, we provide insight into the similarities of the FOXG1 and MECP2 binding partners evolution and function. On the other hand, we suggest that CDKL5 could be a potential candidate for a classical RTT treatment, particularly based on its disordered structure that spans after the catalytic domain to the C-terminus, which shows abundant linear motifs that can bind to molecules with divergent structures of similar affinity. Additionally, we provide insight into the relationship between disordered structure and disease.