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Preprint COMMUNICATION | doi:10.20944/preprints202112.0270.v1

Molecular Characterization of Circulating DENV-2 During Outbreak in Northern Senegal, Rosso 2018

Idrissa Dieng, Mignane Ndiaye, Marie Henriette Ndione, Safietou Sankhe, Moussa Moïse Diagne, Samba Niang Sagne, Aboubacry Gaye, Aliou Barry, Gamou Fall, Amadou Alpha Sall, Cheikh Loucoubar, Oumar Faye, Ousmane Faye

Subject: Biology And Life Sciences, Virology Keywords: Dengue; Dengue virus; cosmopolitan genotype; Senegal; Mauritania; Molecular characterization; Full genome sequencing

Online: 16 December 2021 (12:06:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202110.0287.v1

Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean

Thaís Regina Boufleur, Nelson Sidnei Massola Júnior, Ísis Tikami, Serenella Ana Sukno, Michael Ronald Thon, Riccardo Baroncelli

Subject: Biology And Life Sciences, Plant Sciences Keywords: anthracnose; genome sequencing; pathogenicity factors; Colletotrichum truncatum; Colletotrichum orchidearum; Glomerella; Glycine max

Online: 20 October 2021 (10:11:06 CEST)

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Working Paper ARTICLE

Genome-Wide Study Suggests an Association of the Enhancer rs10419198 for PRR12 Gene with Disordered Eating Behavior in the Mexican Population

José Jaime Martínez-Magaña, Sandra Hernandez, Ana Rosa Garcia, Valeria Cardoso-Barajas, Emmanuel Sarmiento, Beatriz Camarena, Alejandro Caballero, Laura Gonzalez, Jorge Ameth Villatoro-Velazquez, Maria Elena Medina-Mora, Marycarmen Bustos-Gamiño, Clara Fleiz-Bautista, Carlos Alfonso Tovilla-Zarate, Isela Esther Juárez-Rojop, Humberto Nicolini, Alma Delia Genis-Mendoza

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: feeding and eating disorder; genome-wide association study; methylation quantitative trait loci

Online: 8 October 2021 (14:23:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0312.v1

Characterization of Komagataeibacter Isolate Reveals New Prospects on Waste Stream Valorization for Bacterial Cellulose Production

Pietro Cannazza, Antti Rissanen, Dieval Guizelini, Pauli Losoi, Essi Sarlin, Diego Romano, Ville Santala, Rahul Mangayil

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Komagataeibacter rhaeticus; Bacterial cellulose; Crude glycerol; Minimal medium; Whole-genome analysis; Acetate

Online: 16 August 2021 (08:32:19 CEST)

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Preprint REVIEW | doi:10.20944/preprints202107.0045.v1

Insights Gained from Genomic Studies on the Role of Sex Steroids in the Aetiology of Endometriosis

Philippa TK Saunders

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: genome wide association studies (GWAS); single nucleotide polymorphism (SNP); oestrogen; ESR1; HOXA10

Online: 2 July 2021 (09:59:27 CEST)

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Endometriosis is a chronic neuro-inflammatory disorder the defining feature of which is the growth of tissue (lesions) that resembles the endometrium in sites outside the uterus. Estimates of prevalence typically quote rates of ~10% of women of reproductive age, equating to ~190 million women world-wide. Three subtypes of endometriosis are usually considered when discussing the aetiology of the disorder - superficial peritoneal, ovarian (endometrioma cysts), and deep (infiltrating). Genetic, hormonal and immunological factors have all been proposed as contributing to risk factors associated with the development of lesions. Twin studies report the heritable component of endometriosis as ~50%. Genome wide association studies (GWAS) have been conducted allowing unbiased scanning of the genome for single nucleotide polymorphisms (SNPs) in many thousands of individuals. These studies have identified SNPs that appear over-represented in patients with endometriosis, particularly those with more extensive disease (stage III/IV). Amongst the larger scale GWAS there has been replication of SNPs near genes involved in oestrogen and other signalling pathways including ESR1 (oestrogen receptor alpha), GREB1, HOXA10, WNT4 and MAPK kinase signalling. The results from patients with endometriosis have also provided an opportunity to make comparisons with GWAS conducted on other patient cohorts including those with reproductive traits (age at menarche) and disorders (fibroids, endometrial and ovarian cancer) and conditions that are reported by women with endometriosis (migraine, depression). These comparative studies have highlighted some shared genetically-controlled biological mechanisms, including hormone-regulated pathways which might explain the co-occurrence of endometriosis with these disorders. In summary, unbiased genetic analysis has provided new insights into the genetic factors that may contribute to increased risk of developing endometriosis. New studies are needed to broaden the range of patients contributing to these datasets and to improve integration with non-genomic and tissue expression data before their full potential for diagnosis and improvements in patient care can be fully realised.

Preprint ARTICLE | doi:10.20944/preprints202107.0020.v1

Molecular Biology and Pathological Process of an Infectious Bronchitis Virus With Enteric Tropism in Commercial Broilers

Ana Paula da Silva, Ruediger Hauck, Sabrina R.C. Nociti, Colin Kern, H.L. Shivaprasad, Huaijun Zhou, Rodrigo A. Gallardo

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: IBV; infectious bronchitis; variants; whole-genome sequencing, enteric tropism; runting-stunting syndrome

Online: 1 July 2021 (11:25:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0333.v1

Functional Validation of cas9/guideRNA Constructs for Site-directed Mutagenesis of Triticale ABA8’OH1 loci

Krzysztof Michalski, Christian Hertig, Dariusz Mańkowski, Jochen Kumlehn, Janusz Zimny, Anna M. Linkiewicz

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome editing; CRISPR; protoplast; , targeted mutagenesis; TREX2; construct validation; transi-ent expression

Online: 14 May 2021 (13:44:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0473.v1

TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data

Vista Sohrab, Cristina López-Díaz, Antonio Di Pietro, Li-Jun Ma, Dilay Hazal Ayhan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: transposable elements; mobile element insertion events; next generation sequencing (NGS); genome evolution

Online: 18 December 2020 (14:53:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints202009.0559.v1

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Genotypes Circulating in East African Smallholder Pig Farms

Joshua O. Amimo, Eunice M. Machuka, Edward O. Abworo, Anastasia N. Vlasova, Roger Pelle

Subject: Biology And Life Sciences, Virology Keywords: porcine astroviruses; linear antigenic epitopes; recombination; glycosylation; whole genome sequences; East Africa

Online: 24 September 2020 (03:26:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0285.v1

Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus

Sahar Abd El Rahman, Bernd Hoffmann, Reham Karam, Mohamed El-Beskawy, Mohammed F. Hamed, Leonie F. Forth, Dirk Höper, Michael Eschbaumer

Subject: Biology And Life Sciences, Virology Keywords: FMDV; Egypt; full-genome sequencing; interserotypic recombination; vaccine composition analysis; frozen evolution

Online: 12 August 2020 (11:56:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0144.v1

Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic

Alessia Lai, Annalisa Bergna, Sara Caucci, Nicola Clementi, Ilaria Vicenti, Filippo Dragoni, Anna Maria Cattelan, Stefano Menzo, Angelo Pan, Annapaola Callegaro, Adriano Tagliabracci, Arnaldo Caruso, Francesca Caccuri, Silvia Ronchiadin, Claudia Balotta, Maurizio Zazzi, Emanuela Vaccher, Massimo Clementi, Massimo Galli, Gianguglielmo Zehender

Subject: Biology And Life Sciences, Virology Keywords: phylodynamic analyses; SARS-CoV2 circulation in Italy; molecular tracing; Whole Genome Sequencing

Online: 8 July 2020 (11:00:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0181.v1

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Furrukh Mehmood, Abdullah ., Zartasha Ubaid, Yiming Bao, Peter Poczai, Bushra Mirza

Subject: Biology And Life Sciences, Plant Sciences Keywords: Ashwagandha; Chloroplast Genome; InDels; Medicinal plants; Mutational hotspots; Phylogenomics; Solanaceae; Substitutions; Withania

Online: 11 March 2020 (10:21:56 CET)

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Preprint ARTICLE | doi:10.20944/preprints201912.0354.v1

Whole-Genome Sequencing of Lactobacillus Helveticus D75 and D76 Confirms Safety and Probiotic Potential

Vyacheslav Toropov, Elena Demyanova, Olga Shalaeva, Stanislav Sitkin, Timur Vakhitov

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Lactobacillus helveticus; probiotics; whole genome sequencing; PacBio; probiotic genes; bacteriocins; gene expression

Online: 26 December 2019 (10:56:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints201911.0353.v1

Unbiased High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine

Leonie Forth, Dirk Höper, Martin Beer, Michael Eschbaumer

Subject: Biology And Life Sciences, Virology Keywords: inactivated vaccine; vaccine matching; composition; deep sequencing; degraded RNA; FMDV; whole genome

Online: 28 November 2019 (04:03:46 CET)

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Preprint REVIEW | doi:10.20944/preprints201911.0300.v1

Next Generation Biological Control: The Need for Integrating Genetics and Evolution

Kelley Leung, Erica Ras, Kim Ferguson, Simone Ariëns, Dirk Babendreier, Piter Bijma, Kostas Bourtzis, Jacques Brodeur, Margreet Bruins, Alejandra Centurión, Sophie Chattington, Milena Chinchilla-Ramírez, Marcel Dicke, Nina Fatouros, Joel González Cabrera, Thomas Groot, Tim Haye, Markus Knapp, Panagioata Koskinioti, Sophie Le Hesran, Manolis Lirakis, Angeliki Paspati, Meritxell Pérez-Hedo, Wouter Plouvier, Christian Schlötterer, Judith Stahl, Andra Thiel, Alberto Urbaneja, Louis van de Zande, Eveline Verhulst, Louise Vet, Sander Visser, John Werren, Shuwen Xia, Bas Zwaan, Sara Magalhães, Leo Beukeboom, Bart Pannebakker

Subject: Biology And Life Sciences, Insect Science Keywords: artificial selection; biological control; genetics; genome assembly; genomics; insect breeding; microbiome; modelling

Online: 24 November 2019 (17:10:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints201910.0156.v1

Complete Genomic Sequence of Noni mosaic virus (NoMV), a Novel Potyvirus Associated with a Mosaic Disease in Morinda citrifolia L.

Nai-Tong Yu, Zhi-Ying Cai, Zhongguo Xiong, Yan Yang, Zhi-Xin Liu

Subject: Biology And Life Sciences, Virology Keywords: noni mosaic virus; potyvirus; complete genome; morinda citrifolia l; illumina transcriptomic sequencing

Online: 14 October 2019 (09:29:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0154.v1

Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways

Aayushi Srivastava, Abhishek Kumar, Sara Giangiobbe, Elena Bonora, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: papillary thyroid cancer; germline mutations; whole genome sequencing; predisposition markers; pathway analysis

Online: 13 October 2019 (17:07:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0147.v1

Whole Genome Alignment Based Development of Molecular Marker for Detecting Leptosphaeria maculans and Leptosphaeria biglobosa, the Causal Agent of Blackleg Disease in Brassicas

Mostari Jahan Ferdous, Mohammad Rashed Hossain, Denison Michael Immanuel Jesse, Jong-In Park, Hee-Jeong Jung, Hoy-Taek Kim, Ill-Sup Nou

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: blackleg; brassica; diagnosis; effector; genome alignment; leptosphaeria biglobosa; leptosphaeria maculans; marker; PCR

Online: 13 October 2019 (16:08:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0297.v1

Development of a Transformation Method for Metschnikowia borealis and Other CUG-Serine Yeasts

Zachary Gordon, Maximillian P. M. Soltysiak, Christopher Leichthammer, Jasmine A. Therrien, Rebecca S. Meaney, Carolyn Lauzon, Matthew Adams, Dong Kyung Lee, Preetam Janakirama, Marc-Andre Lachance, Bogumil J. Karas

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genome engineering; synthetic biology; yeasts; Metschnikowia; genetic tools; DNA delivery; CUG-Ser

Online: 13 November 2018 (05:17:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints201810.0638.v1

Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae)

Luoyun Wang, Jing Wang, Caiyun He, Jianguo Zhang, Yanfei Zeng

Subject: Biology And Life Sciences, Plant Sciences Keywords: Chloroplast genome; H. gyantsensis; H. rhamnoides subsp. yunnanensis; Ka/ks; Optimal codons

Online: 26 October 2018 (15:40:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0169.v1

“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome and Nutrigenomics of the European Sardine, Sardina pilchardus

André M. Machado, Ole K. Tørresen, Naoki Kabeya, Alvarina Couto, Bent Petersen, Mónica Felício, Paula F. Campos, Elza Fonseca, Narcisa Bandarra, Mónica Lopes-Marques, Renato Ferraz, Raquel Ruivo, Miguel M. Fonseca, Sissel Jentoft, Óscar Monroig, Rute Da Fonseca, L. Filipe C. Castro

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: European sardine; draft genome; teleosts; comparative genomics; long chain polyunsaturated fatty acids

Online: 10 September 2018 (12:37:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201705.0206.v1

Genome Characterization of a Novel Binary Toxin-Positive Strain of Clostridium difficile and Comparison with the Epidemic 027 and 078 Strains

Zhong Peng, Sidi Liu, Xiujuan Meng, Wan Liang, Biao Tang, Yuanguo Wang, Juping Duan, Chenchao Fu, Bin Wu, Anhua Wu, Chunhui Li

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Clostridium difficile; ST201; binary toxin-positive; whole genome sequencing; comparative genomic analysis

Online: 30 May 2017 (06:15:11 CEST)

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A novel binary toxin-positive non-027, non-078 Clostridium difficile strain designated LC693 whose sequence type was ST201 was isolated from the fecal sample of a patient with severe diarrhea in China. To understand the pathogenesis basis of C. difficile ST201, this recently recovered isolate LC693 was then chosen for whole genome sequencing. The project finally generated an estimated genome size of approximately 4.07 Mbp. The genome sequence was then analyzed together with the other two ST201 strains VL-0104 and VL-0391 and compared to the epidemic 027/ST1 and 078/ST11 strains. Phylogenetic analysis demonstrated that the ST201 strains belonged to clade 3. Genome size of the three ST201 strains ranged from 4.07 Mb~4.16 Mb, with an average GC content between 28.5%~28.9%. The ST201 genomes contained more than 40 antibiotic resistance genes and 15 of them were predicted to be associated with vancomycin-resistance, suggesting that they may have a strong antibiotic resistance. The ST201 strains contained a typical clade 3 specific PaLoc with a Tn6218 element inserted, and those genes harbored on their PaLoc that participated in the toxin expression and regulation were highly homologues to the epidemic 027 and 078 strains, with the exception of tcdC. A truncated TcdC was found in the ST201 strains, which is suggestive to have a contribution to the toxin production of the ST201 strains. In addition, the ST201 strains contained intact binary toxin coding and regulation genes, which is also proposed to contribute to the virulence. Genome comparison of the ST201 strains with the epidemic 027 and 078 strain identified 641 genes specific for the C. difficile ST201, and a number of them were predicted as fitness and virulence associated genes. The identification of those genes also contributes to the pathogenesis of the ST201 strain. To our knowledge, this is the first study that the genome sequence of C. difficile ST201 was discussed in detail, and the present study would have a contribution to understanding the pathogenesis basis of C. difficile ST201.

Preprint ARTICLE | doi:10.20944/preprints202312.0701.v1

Increasing the Activity of the High-Fidelity SpyCas9 Form in Yeast by Directed Mutagenesis of the PAM Interacting Domain

Artem I Davletshin, Anna A Matveeva, Stanislav S Bachurin, Dmitry S Karpov, David G Garbuz

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Saccharomyces cerevisiae; genome editing; site-directed mutagenesis; CRISPR/Cas9; high-fidelity Cas9 forms

Online: 12 December 2023 (07:43:14 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202311.0774.v1

Syncytial Nets vs. Chemical Signaling: Emerging Properties of Alternative Integrative Systems

Leonid Moroz

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Ctenophora; Porifera; Placozoa; Cnidaria; nervous system evolution; neurotransmission; synapses; animal origins; genome; behavior

Online: 13 November 2023 (10:27:17 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.1057.v1

An Outbreak of Vancomycin-Resistant Enterococci in a City Hospital Intensive Care Unit: Molecular Characterization of Resistance

Feray Ferda Şenol, Elif Seren Tanrıverdi, Zulal Aşçı Toraman, Barış Otlu

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: vancomycin-resistant enterococcus faecium; hospital epidemic; whole genome analysis; infection prevention and control

Online: 15 September 2023 (11:41:52 CEST)

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Vancomisin resistant enterococcus(VRE), is a resistant microorganism which colonizates and causes infections in hospitalized patients. It was aimed to show the spread of vancomycin-resistant Enterococcus (fVREfm) step-by-step in all intensive care units, which started with the growth of vancomycin-resistant Enterococcus faecium (VREfm) on 02.12.2021 in the blood culture of a patient hospitalized in the anesthesia intensive care unit of our hospital and was found to have reached epidemic size in the surveys. Rectal swab samples were taken from all patients hospitalized in intensive care units, VRE colonization was determined and the VanA and VanB resistance genes associated with vancomycin resistance of VREfm isolates were determined by PCR method, and clonal association analysis was performed by Arbitrarily Primed-PCR (AP-PCR) and Pulsed-Field Gel Electrophoresis. In our study, VRE was detected in 61 of 2601 rectal swab samples. 54 (85.52%) of the VRE isolates were Enterococcus faecium, 3 (4.91%) was Enterococcus faecalis, 3 (4.91%) was Enterococcus gallinorum, 1 (1.63%) was Enterococcus casseliflavus. It was determined that all of the 54 VREfm isolates, which were the most detected among all VRE isolates, carried the vanA gene. In the clonal association analysis of the isolates by AP-PCR and PFGE methods, it was found that they had 12 different genotypes, 48 of them were included in any cluster, the clustering rate was 88.8%, and the largest cluster was genotype 1 cluster with 36 isolates. Of the 54 patients with VREfm isolated recently, 18.51 percent of the clinical samples were isolated before the survey, and 9.24% were isolated after the survey. It was determined that 100% of VREfm isolates were resistant to ampicillin, levofloxacin, ciprofloxacin, high-level gentamicin, trimethoprim-sulfamethoxazole, teicoplanin, 7.4% to tigecycline and 1.85% to linezolid. In our study, in the clonal association analysis performed by isolating VREfm in rectal swab samples, it was found that 88.8% of the samples were indistinguishably similar and the increase in the number of VREfm infections after the index case in our hospital was associated with the epidemic. VREfm infections cause long term hospitalization, costs and also deaths, which shows the seriousness of the event, and the importance of the combination of epidemiological and molecular analysis in epidemic research.

Preprint ARTICLE | doi:10.20944/preprints202308.0658.v1

Validation and cross-species transferability of SSR markers developed from whole genome sequence (WGS) of Mungbean (Vigna radiata L. Wilczek) and their application of population genetics in Vigna species

Pawan Saini, Tejinderjit Singh Bains, Asmita Sirari, Inderjit Singh Yadav, Kamalpreet Singh Mandahal, Sayeed Abdul Hamid Patel, Javed Akhatar, Navkiran Ludhar, Pooja Saini, Sharon Nagpal, Aditya Pratap

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Mungbean, Vigna, Whole genome sequence, SSR markers, Principal co-ordinate analysis, Genetic diversity

Online: 8 August 2023 (11:23:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0010.v1

CoVigator – a Knowledge Base for Navigating SARS-CoV-2 Genomic Variants

Thomas Bukur, Pablo Riesgo-Ferreiro, Patrick Sorn, Ranganath Gudimella, Johannes Hausmann, Thomas Rösler, Martin Löwer, Barbara Schrörs, Ugur Sahin

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: SARS-CoV-2; dashboard; genomic variants; software; pipeline; virus genome assemblies; knowledge base

Online: 1 June 2023 (03:16:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints202212.0582.v1

COVID-19: The Ethno-Geographic Perspective of Differential Immunity

Usman Abdullah, Ned Saleh, Peter Shaw, Nasir Jalal

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; copy number variation (CNV); virome; microbiome; endoretroviral genome (ERV); geographic disparity

Online: 30 December 2022 (10:00:27 CET)

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Preprint ARTICLE | doi:10.20944/preprints202212.0232.v1

Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies

Alexandre Hassanin, Opale Rambaud

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)

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Preprint REVIEW | doi:10.20944/preprints202211.0169.v1

Resistance and Tolerance to Viroid Infection

Takashi Naoi, Shifang Li, Teruo Sano

Subject: Biology And Life Sciences, Virology Keywords: viroid; resistance; tolerance; RNA silencing; plant hormone; spray-induced gene silencing; genome editing

Online: 9 November 2022 (03:10:00 CET)

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Preprint HYPOTHESIS | doi:10.20944/preprints202206.0409.v1

Evolutionary Honing in and Mutational Replacement: How Long-Term Directed Mutational Responses to Specific Environmental Pressures Are Possible

Adi Livnat, Daniel Melamed

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Non random mutation; interaction-based evolution; hemoglobin S; directed mutation; parallelism; genome organization

Online: 29 June 2022 (14:56:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0051.v1

Genetic Knockouts Indicate That the ABCC2 Gene in the Bollworm Helicoverpa Zea Is Not a Major Receptor for the Cry1Ac Insecticidal Protein.

Omaththage P. Perera, Nathan S LIttle, Heba Abdelgaffar, Juan Luis Jurat-Fuentes, Gadi V. P. Reddy

Subject: Biology And Life Sciences, Insect Science Keywords: Helicoverpa zea; Bollworm; CRISPR; Cry1A; Bt Toxin; Genome Editing; Knockout; Functional Genomics; Resistance

Online: 3 September 2021 (08:19:44 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0244.v1

Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus

Alina Renz, Andreas Dräger

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Staphylococcus aureus; MRSA; genome-scale metabolic models; model-driven discovery; strain-specific models

Online: 8 April 2021 (14:25:31 CEST)

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Working Paper REVIEW

Discoveries and Biological Implications of Mammalian 45S rDNA Variants and Non-Structural rRNAs

Yih-Horng Shiao

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Ribosomal DNA; ribosomal RNA; mammalian genome; intra- and inter-individual variations; development; diseases.

Online: 26 February 2021 (11:35:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202005.0463.v3

Trends of Mutation Accumulation Across Global SARS-CoV-2 Genomes: Implications for the Evolution of the Novel Coronavirus

Chayan Roy, Santi M Mandal, Suresh K Mondol, Shriparna Mukherjee, Wriddhiman Ghosh, Ranadhir Chakraborty

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; genome-wide mutations; transition; transversion; nonsynonymous and synonymous mutations; microevolution

Online: 5 October 2020 (10:56:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202003.0351.v1

Genome Editing: An Emerging Tool for Plant Breeders

Anand Kumar, Karansher Sandhu

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Conventional method; Clustered Regularly Interspaced Short Palindromic Sequence; Genome editing; RNA Interference; TALEN

Online: 23 March 2020 (10:23:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints201904.0085.v2

Meta-Analysis of Cancer Triploidy: Whole-Genome Rearrangements in Male Human Tumours Are Characterised by XXY Karyotypes

Ninel M. Vainshelbaum, Pawel Zayakin, Regina Kleina, Alessandro Giuliani, Jekaterina Erenpreisa

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: cancer near-triploidy; male tumours; karyotype meta-analysis; XXY; whole genome rearrangements; digyny

Online: 14 July 2019 (09:25:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201902.0035.v1

Characterization of a Bbotybirnavirus Conferring Hypovirulence in the Pear Stem Wart Disease Phytopathogenic Fungus Botryosphaeria dothidea

Lifeng Zhai, Mengmeng Yang, Meixing Zhang, Ni Hong, Guoping Wang

Subject: Biology And Life Sciences, Virology Keywords: Botryosphaeria dothidea botybirnavirus 1; Hypovirulence; Botybirnavirus; Genome; Botryosphaeria dothidea; double-stranded RNA virus

Online: 4 February 2019 (13:44:22 CET)

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Preprint REVIEW | doi:10.20944/preprints201812.0156.v1

The Report of Marine Life Genomic Research

Guangyi Fan, Jianwei Chen, Tao Jin, Chengcheng Shi, Xiao Du, He Zhang, Yaolei Zhang, Hanbo Li, Ting Luo, Pengxu Yan, Guang Liu, Xiangqun Chi, Xiaoxuan Tan, Liangwei Li, Guilin Liu, Xiaochuan Liu, Shijie Hao, Kai Han, Xiaoyun Huang, Shuai Sun, Jing Zhou, Mengjun Yu, Lingfeng Meng, Yue Chang, Rui Zhang, Kaiqiang Liu, Mengqi Zhang, Yong Zhao, Chang Li, Jiao Guo, Xinyu Guo, Jiahao Wang, Meiqi Lv, Haoyang Gao, Yujie Liu, Yue Song, Shengjun Wang, Yang Deng, Binjie Ouyang, Jinzhong Lin, Yingjia Yu, lynn Fink, Xianwei Yang, Xun Xu, Xin Liu

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Marine microorganisms, marine fungi, algae, marine plants, marine invertebrates, marine vertebrates, genome, metagenome

Online: 12 December 2018 (15:44:09 CET)

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Preprint REVIEW | doi:10.20944/preprints201808.0089.v1

Molecular and Genetic Bases of Fruit Firmness Variation in Blueberry—A Review

Francesco Cappai, Juliana Benevenuto, Luis Felipe V. Ferrao, Patricio Munoz

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: firmness; Vaccinium; ripening; cell wall; crispy; quantitative genetics; breeding; molecular markers; genome editing

Online: 5 August 2018 (10:11:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0054.v1

Neuronal Ceroid Lipofuscinosis in a Mixed Breed Dog with a Splice Site Variant in CLN6

Tendai Mhlanga-Mutangadura, Garrett Bullock, Sofia Cerda-Gonzalez, Martin L Katz

Subject: Animal Science, Veterinary Science And Zoology, Biology And Life Sciences Keywords: neurodegeneration; lysosomal storage; mitochondrial subunit c protein; lipofusciin; fluorescence; whole genome sequencing; electron microscopy

Online: 1 May 2024 (08:15:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1298.v1

Machine Intelligence with Associative Memory and Event-Driven Transaction History

Rao Mikkilineni, W. Patrick Kelly

Subject: Artificial Intelligence And Machine Learning, Computer Science And Mathematics Keywords: Machine Intelligence; Associative Memory; Event-Driven Transaction History; Self-Regulation; Digital Genome; Autopoiesis; Cognition

Online: 19 April 2024 (14:57:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1209.v1

Genetic Characterization and Population Structure of Drug Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing

Leonardo Souza Esteves, Lia Lima Gomes, Daniela Brites, Fátima Cristina Onofre Fandinho, Marcela Bhering, Márcia Aparecida da Silva Pereira, Emilyn Costa Conceição Sharma, Richard Salvato, Bianca Porphirio da Costa, Reginalda Ferreira de Melo Medeiros, Paulo Cesar de Souza Caldas, Paulo Redner, Margareth Pretti Dalcolmo, Vegard Eldholm, Sebastien Gagneux, Maria Lucia Rossetti, Afrânio Lineu Kritski, Philip Noel Suffys

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Mycobacterium tuberculosis; Drug Resistance; Whole Genome Sequencing; Genetic Diversity; Brazil; Novel Mutations

Online: 18 April 2024 (07:51:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.1500.v1

Genome-Wide Association Study for Biomass Yield and Feed Quality in Buffel Grass (Cenchrus ciliaris L.)

Alemayehu Teressa Negawo, Meki Shehabu Muktar, Ricardo Alonso Sánchez Gutiérrez, Ermias Habte, Alice Muchugi, Chirs S. Jones

Subject: Biology And Life Sciences, Plant Sciences Keywords: Buffel grass, Genome-wide association study, Tropical forage, Forage improvement, Genetic resources, drought tolerance

Online: 20 December 2023 (09:52:12 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0929.v1

Comparative Genomic Analysis of Colletotrichum lini Strains with Different Virulence on Flax

Ekaterina M. Dvorianinova, Elizaveta A. Sigova, Timur D. Mollaev, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Roman O. Novakovskiy, Anastasia A. Turba, Daiana A. Zhernova, Elena V. Borkhert, Elena N. Pushkova, Nataliya V. Melnikova, Alexey A. Dmitriev

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Colletotrichum lini; anthracnose; flax pathogen; virulence; Nanopore sequencing; de novo genome assembly

Online: 13 December 2023 (05:07:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0628.v1

A Knockout of the IFITM3 Gene Increases the Sensitivity of WI-38 VA13 Cells to the Influenza a Virus

Natalya Eshchenko, Mariia Sergeeva, Evgenii Zhuravlev, Kira Kudria, Elena Goncharova, Andrey Komissarov, Grigory Stepanov

Subject: Biology And Life Sciences, Virology Keywords: IFITM; Influenza A virus; Human cells; WI-38; Genome editing; CRISPR/Cas9; RNA-seq

Online: 8 December 2023 (12:42:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.1454.v1

Whole Genome Sequencing Uncovers the Genetic Determinants of Colistin Resistance in Multi-Drug Resistant Klebsiella pneumoniae Isolated from Patients Admitted in the ICU of a Tertiary Care Hospital in Kampala, Uganda

Maximilian A. K. Magulye, Reuben S. Maghembe, Simon Sekyanzi, Beatrice Achan, Savannah Mwesigwa, Eric Katagirya

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Klebsiella pneumoniae, whole genome sequences (WGS), antimicrobial resistance (AMR), multidrug resistance (MDR), colistin resistance

Online: 23 October 2023 (13:26:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0727.v1

Differential Large and Small Terminase Subunit Assembly Mediate Bacteriophage P22 Genome Packaging

Julia Elise Cabral, Yanfei Qiu, Abert J.R. Heck, Reginald McNulty

Subject: Biology And Life Sciences, Virology Keywords: Salmonella virus; viral genome-packaging motor; small terminase; large terminase; Bacteriophage P22; electron microscopy

Online: 12 September 2023 (04:43:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.2105.v1

Whole-Genome Sequencing-Based Screening of Methicillin Resistant Staphylococcus aureus in Patients and Healthcare Workers in Public Hospitals in Benin

Carine Laurence Yehouenou, Bert Bogaerts, Kevin Vanneste, Sigrid C.J. De Keersmaecker, Nancy H.C. Roosens, Arsène A. Kpangon, Dissou Affolabi, Anne Simon, Francis Moise Dossou, Olivia Dalleur

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Methicillin-resistant Staphylococcus aureus; healthcare workers; whole genome sequencing; low-or middle-income countries

Online: 29 June 2023 (12:46:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0270.v1

Genomic Analysis of Infectious Bursal Disease Virus in Nigeria: Identification of Unique Mutations of Yet Unknown Biological Functions in Both Segments A and B

Ijeoma Nwagbo, Adelaide Milani, Annalisa Salviato, Gianpiero Zamperin, Lanre Sulaiman, Nanven Maurice, Clement Meseko, Alice Fusaro, Ismaila Shittu

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)

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Preprint REVIEW | doi:10.20944/preprints202211.0430.v1

Attenuation and Degeneration of SARS-CoV-2 Despite of Adaptive Evolution

Yingguang Liu

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2, evolution, immune evasion, codon usage, attenuation, genome degradation, degeneration, COVID-19

Online: 23 November 2022 (03:29:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202211.0059.v1

Genomic Epidemiology of SARS-Cov-2 in Western Burkina Faso, West Africa

Yacouba Sawadogo, Lokman Galal, Essia Belarbi, Arsène Zongo, Grit Schubert, Fabian Leendertz, Abdoulie Kanteh, Abdul Karim Sesay, Annette Erhart, Anne-Laure Bañuls, Zekiba Tarnagda, Sylvain Godreuil, Halidou Tinto, Abdoul-Salam Ouedraogo

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Whole Genome Sequencing; Genomic epidemiology; West Africa, Burkina Faso

Online: 2 November 2022 (11:14:27 CET)

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Preprint REVIEW | doi:10.20944/preprints202210.0313.v1

The Complex World of Emaraviruses – Challenges, Insights and Prospects

Marius Rehanek, David G. Karlin, Martina Bandte, Rim Al Kubrusli, Shaheen Nourinejhad Zarghani, Thierry Candresse, Carmen Büttner, Susanne Von Bargen

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)

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Preprint REVIEW | doi:10.20944/preprints202103.0717.v1

Role of the Non-Canonical RNAi Pathway in the Antifungal Resistance and Virulence of Mucorales

José Tomás Cánovas-Márquez, María Isabel Navarro-Mendoza, Carlos Pérez-Arques, Carlos Lax, Ghizlane Tahiri, José Antonio Pérez-Ruiz1, Damaris Lorenzo-Gutiérrez, Silvia Calo, Sergio López-García, Eusebio Navarro, Francisco Esteban Nicolás, Victoriano Garre, Laura Murcia-Flores

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: virulence; antifungal resistance; non-canonical RNAi; epimutant; R3B2; RdRP; transposon; genome stability; Mucorales; mucormycosis.

Online: 30 March 2021 (09:37:39 CEST)

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Preprint REVIEW | doi:10.20944/preprints202009.0548.v1

Metabolic Modelling Approaches for Describing and Engineering Microbial Communities

Beatriz García-Jiménez, Jesús Torres, Juan Nogales

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genome-scale metabolic model; microbial community; optimization; design; engineering; computational methods; synthetic microbial consortia

Online: 23 September 2020 (09:52:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0002.v1

Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics

Michael Gruenstaeudl

Subject: Biology And Life Sciences, Plant Sciences Keywords: codon position; complete chloroplast; early-diverging angiosperms; monophyly; Nymphaeaceae; Nymphaeales; plastid genome; phylogenomics; repeatability

Online: 3 May 2019 (14:03:46 CEST)

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The monophyly of Nymphaeaceae (water lilies) represents a critical question in understanding the evolutionary history of early-diverging angiosperms. A recent plastid phylogenomic investigation claimed new evidence for the monophyly of Nymphaeaceae, but its results could not be verified from the available data. Moreover, preliminary gene-wise analyses of the same dataset provided partial support for the paraphyly of the family. The present investigation aims to re-assess the previous conclusion of the monophyly of Nymphaeaceae under the same dataset and to determine the congruence of the phylogenetic signal across different plastome genes and data partition strategies. To that end, phylogenetic tree inference is conducted on each of 78 protein-coding plastome genes, both individually and upon concatenation, and under four data partitioning schemes. Moreover, the possible effects of various sequence variability and homoplasy metrics on the inference of specific phylogenetic relationships are tested using multiple logistic regression. Differences in the variability of polymorphic sites across codon positions are assessed using parametric and non-parametric analysis of variance. The results of the phylogenetic reconstructions indicate considerable incongruence among the different gene trees as well as the data partitioning schemes. The results of the multiple logistic regression tests indicate that the fraction of polymorphic sites of codon position 3 has a significant effect on the recovery of the monophyly of Nymphaeaceae. Taken together, these results indicate that the monophyly of Nymphaeaceae currently remains indeterminate, and that specific phylogenetic conclusions are strongly dependent on the precise plastome gene, data partitioning scheme, and codon position evaluated. In closing, I discuss the importance of archiving all data of an investigation in publicly accessible data repositories, along with sufficient details to replicate the published results, and provide recommendations on future plastid phylogenomic investigations of Nymphaeales.

Preprint ARTICLE | doi:10.20944/preprints201810.0505.v1

Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter Kameinonensis and Mucilaginibacter Rubeus Isolated from a Gold/Copper Mine

Yuan Ping Li, Nicolas Carraro, Nan Yang, Bixiu Liu, Xian Xia, Renwei Feng, Quaiser Saquib, Hend A. Al-Wathnani, Jan Roloef van der Meer, Christopher Rensing

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Mucilaginibacer rubeus；Mucilaginibacter kameinonensis; genomic island; evolution; heavy metal resistance; draft genome sequence; CTnDOT

Online: 22 October 2018 (15:21:18 CEST)

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Preprint REVIEW | doi:10.20944/preprints201709.0163.v1

From Genotype to Phenotype: A Clinical Perspective for Hospital-Acquired Pneumonia

Etienne Ruppé, Abdessalam Cherkaoui, Vladimir Lazarevic, Stéphane Emonet, Jacques Schrenzel

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: next-generation sequencing; whole-genome sequencing; hospital-acquired pneumonia; antibiotic resistance; prediction; clinical metagenomics

Online: 30 September 2017 (04:49:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201607.0096.v1

Prokaryotic gene-family size correlations

Gon Carmi, Alexander Bolshoy

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: number of paralogs; comparative genomics; combinatorial optimization; Mycoplasmas; Halophiles; Orientia; Mycobacterium leprae; genome size

Online: 29 July 2016 (16:24:29 CEST)

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Preprint REVIEW | doi:10.20944/preprints202403.1124.v1

A Unifying Hypothesis for the Genome Dynamics Proposed to Underly Neuropsychiatric Phenotypes

George Sebastian Gericke

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: common fragile sites; stress; mobile elements; immune; RAG 1/2; genome plasticity; neuropsychiatric; GWAS; epigenetic

Online: 22 March 2024 (07:46:57 CET)

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Preprint ARTICLE | doi:10.20944/preprints202403.0136.v1

Integrating Genome-Scale Metabolic Models with Patient Plasma Metabolome to Study Endothelial Metabolism In Situ

Fernando Silva-Lance, Isabel Montejano-Montelongo, Eric Bautista, Lars K. Nielsen, Pär I. Johansson, Igor Marin de Mas

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Metabolic Network Analysis; Genome-Scale Metabolic Models; Exo-Metabolomics Integration; Sampling Algorithms; Endothelial Cell Metabolism

Online: 4 March 2024 (14:02:11 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0623.v1

Genome Analysis of Epsilon Crass-like Phages Revealed That Some of Them Can Be Temperate Phages Encoding Atypical Diversity-Generating Retroelements

Igor V. Babkin, Artem Y. Tikunov, Ivan K. Baykov, Vera V. Morozova, Nina V. Tikunova

Subject: Biology And Life Sciences, Virology Keywords: crAss-like phages; genome sequence; diversity-generating retroelements; temperate phages; phylogenetics; virus taxonomy; 3D modeling

Online: 8 December 2023 (13:28:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.0748.v1

SARS-CoV-2 Omicron Variants and Their Susceptibility Towards Monoclonal Antibodies in a Swedish Cohort During 2022-23, Studied by Next-Generation Sequencing

Jonathan Haars, Navaneethan Palanisamy, Frans Wallin, Paula Mölling, Johan Lindh, Martin Sundqvist, Patrik Ellström, René Kaden, Johan Lennerstrand

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; coronavirus; monoclonal antibodies; resistance; nanopore; Sweden; whole-genome sequencing; receptor binding domain

Online: 12 September 2023 (11:14:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0094.v1

Sustainable Metabolic Engineering Design Development Employing a Complex Objective Function

Reinis Muiznieks, Elina Dace, Egils Stalidzans

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: economic sustainability; environmental sustainability; social sustainability; genome scale metabolic model; metabolic engineering; growth coupled production

Online: 3 May 2023 (04:32:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0961.v1

Whole Genome Sequence Analysis of SARS-COV-2 Isolated from COVID-19 Patients in Duhok Province, Iraq

Sherzad Majeed Taher, Jassim Mohammed Abdo, Muayad Aghali Merza

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)

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Preprint REVIEW | doi:10.20944/preprints202208.0154.v1

Integrated Genetic and Omics Approaches for the Regulation of Nutritional Activities in Rice (Oryza sativa L.)

Muhammad Junaid Zaghum, Kashir Ali, Sheng Teng

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Genome selection; Rice breeding; Genetic analysis; Omics assisted markers; Nutritional quality; Genomics and pangenomics; Biofortification

Online: 8 August 2022 (10:53:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0255.v1

First Genomic Insights Into The Mandevilla Genus

Fabio Palumbo, Samela Draga, Francesco Scariolo, Gio Batta Sacilotto, Marco Gazzola, Gianni Barcaccia

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome assembly; Apocynaceae; SSR; superbarcoding; flow cytometry; monoterpene indole alkaloids; DNA barcoding; cpDNA; Mandevilla sanderi

Online: 27 April 2022 (10:07:43 CEST)

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Preprint REVIEW | doi:10.20944/preprints202202.0224.v1

Omicron Variant: Secrets Behind the Great Escape Artist

Henry Sutanto, Djoko Santoso

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; pandemic; SARS-CoV-2; Omicron variant; emerging disease; global health; virus; genome; mutation

Online: 18 February 2022 (05:23:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202110.0246.v1

The Complete Chloroplast Genome Sequence of Four Plant Species, Their SSR Identification and Phylogenetic Analysis

Yueyi Zhu, Xianwen Zhang, Guopeng Li, Jiqian Xiang, Jinghua Su, Liwen Wu, Muhammad Khan Daud, Lei Mei

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)

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Preprint ARTICLE | doi:10.20944/preprints202011.0685.v1

Fitting Together the Evolutionary Puzzle pieces of the Immunoglobulin T Gene from Antarctic Fishes

Alessia Ametrano, Marco Gerdol, Maria Vitale, Samuele Greco, Umberto Oreste, Maria Roria Coscia

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: teleost fish; Notothenioidei; genome modifications; IgT; exonic remnant; immunoglobulin domain; Antarctic marine environment; molecular evolution

Online: 27 November 2020 (11:31:09 CET)

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Preprint REVIEW | doi:10.20944/preprints202011.0667.v1

Conventional Breeding, Molecular Breeding and Speed Breeding; Brave Approaches to Revamp the Production of Cereal Crops

Muhammad Haroon, Muhammad Mubashar Zafar, Muhammad Awais Farooq, Rabail Afzal, Maria Batool, Fahad Idrees, Usman Babar, Abdu Saboor Khan, Huijuan Mo, Lin Li, Maozhi Ren

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Plant breeding; Genome editing; Molecular breeding; Prime editing; Base editing; CRISPR Cas; Epigenetics; Speed breeding

Online: 26 November 2020 (11:17:56 CET)

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Preprint REVIEW | doi:10.20944/preprints202008.0007.v1

The Genome in a Three-Dimensional Context: Deciphering the Contribution of Noncoding Mutations at Enhancers to Blood Cancer

Llorenç Rovirosa-Mulet, Alberto Ramos-Morales, Biola M. Javierre

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: spatial genome architecture; 3D chromatin organization; DNA loops; noncoding mutations; enhancer; blood cancer; hematopoietic malignancies

Online: 2 August 2020 (09:33:40 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202004.0253.v1

Optimizing Open Data to Support One Health: Best Practices to Ensure Interoperability of Genomic Data from Microbial Pathogens

Ruth E. Timme, William J. Wolfgang, Maria Balkey, Sai Laxmi Gubbala Venkata, Robyn Randolph, Marc Allard, Errol Strain

Subject: Biology And Life Sciences, Virology Keywords: Genomic Epidemiology; GenomeTrakr; microbial pathogen surveillance, NCBI submission; whole genome sequencing; QA/QC; One Health

Online: 16 April 2020 (05:26:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0258.v2

Asians Do Not Exhibit Elevated Expression or Unique Genetic Polymorphisms for ACE2, the Cell-Entry Receptor of SARS-CoV-2

Ying Chen, Kejia Shan, Wenfeng Qian

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; cell-entry receptor; ACE2; The Cancer Genome Atlas; susceptibility; demographic factors; polymorphism

Online: 25 February 2020 (06:30:17 CET)

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Preprint ARTICLE | doi:10.20944/preprints201808.0539.v1

Genotype Fingerprints Enable Fast and Private Comparison of Genetic Testing Results for Research and Direct-to-Consumer Applications

Max Robinson, Gustavo Glusman

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: computational genomics; genome comparison; algorithms; genetic testing; privacy; direct-to-consumer; study design; population genetics

Online: 31 August 2018 (04:59:28 CEST)

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Preprint REVIEW | doi:10.20944/preprints202402.0255.v2

Environmental Risk Assessment Scenarios of Specific NGT Applications in Brassicaceae Oilseed Plants

Franziska Koller, Michael Cieslak, Andreas Bauer-Panskus

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: new genomic techniques (NGT); genetically engineered organisms; genome editing; risk assessment; unintended effects in NGT plants

Online: 6 February 2024 (13:40:47 CET)

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Preprint ARTICLE | doi:10.20944/preprints202402.0223.v1

Sequence and Biochemical Analysis of Vaccinia Virus A32 Protein: Implications for In Vitro Stability and Coiled-Coil Motif Mediated Regulation of the DNA-Dependent ATPase Activity

Uma Ramakrishnan, Tanvi Aggarwal, Kiran Kondabagil

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Genome packaging ATPase; vaccinia virus; coiled coil motif; FtsK/HerA superfamily; Nucleo-cytoplasmic large DNA viruses

Online: 5 February 2024 (07:48:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.1020.v1

Listeria monocytogenes ST37 Distribution in Russia and Properties of the Clinical and Food-Born Isolates

Olga L. Voronina, Marina S. Kunda, Natalia N. Ryzhova, Ekaterina I. Aksenova, Margarita A. Kustova, Tatyana I. Karpova, Alina R Melkumyan, Elena A. Klimova, Olga A. Gruzdeva, Igor S. Tartakovsky

Subject: Biology And Life Sciences, Life Sciences Keywords: Listeria monocytogenes; food-born pathogen; invasive listeriosis; cgMLST; whole genome sequencing; prophages; virulence factors; COVID-19.

Online: 14 September 2023 (14:51:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0241.v1

Integrating Genetic and Chromosome Maps of Allium Cepa: From Markers Visualization to Genome Assembly Verification

Aleksey Ermolaev, Natalia Kudryavtseva, Anton Pivovarov, Ilya Kirov, Gennady Karlov, Ludmila Khrustaleva

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Tyr-FISH; integration genetic; cytogenetic and pseudochromosome maps; transcript based markers; genome assembly; bioinformatics; Allium cepa

Online: 12 August 2022 (12:54:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202111.0386.v1

Meta-Analysis of Transcriptome-Wide Association Studies Across 13 Brain Tissues Identified Novel Clusters of Genes Associated with Nicotine Addiction

Zhenyao Ye, Chen Mo, Hongjie Ke, Qi Yan, Chixiang Chen, Elliot L Hong, Peter Kochunov, Braxton D Mitchell, Shuo Chen, Tianzhou Ma

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome-wide association study; transcriptome-wide association study; meta-analysis; expression quantitative trait loci; nicotine addiction

Online: 22 November 2021 (11:46:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202104.0607.v1

A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps

Natalya Kudryavtseva, Aleksey Ermolaev, Gennady Karlov, Ilya Kirov, Masayoshi Shigyo, Shusei Sato, Ludmila Khrustaleva

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Tyr-FISH; plant chromosome preparation; recombinant and cytogenetic maps; transcript-based markers; genome assembly; Allium cepa

Online: 22 April 2021 (12:19:32 CEST)

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Working Paper REVIEW

Advances in Engineering CRISPR-Cas9 as a Molecular Swiss Army Knife

Grace A. Meaker, Emma J. Hair, Thomas E. Gorochowski

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: synthetic biology; CRISPR; Cas9; biotechnology; biodesign; nickase; base editing; prime editing; genome editing; ethics; responsible innovation

Online: 1 October 2020 (08:38:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints201911.0252.v1

From Sequence to Information

Ovidiu Popa, Ellen Oldenburg, Oliver Ebenhöh

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: data; sequence; information; entropy; genome; gene; proteins; time-series; modeling; meta-genomics; transcriptomics; proteomics; bioinformatics; DNA

Online: 22 November 2019 (02:28:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints201808.0187.v1

Possibility of Gene Rearrangement between Porcine Rotavirus H and Porcine Rotavirus C in Nonstructural Protein 3

Tohru Suzuki, Daisuke Inoue

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: Porcine rotavirus H; Porcine rotavirus C; Full genome; Classification; Genotype; Non-structural protein 3; Gene rearrangement

Online: 9 August 2018 (11:38:44 CEST)

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Preprint REVIEW | doi:10.20944/preprints202402.0085.v1

Crispr-cas System: Classification, Benefits, Applications And Function

Taha Nazir, Hameed A. Mirza, Nida Taha

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: CRISPR-Cas System, Biomedicine, Genome engineering, Gene editing, Human disease, Cancer, Animal models Concerns, Benefits, Applications, Function

Online: 1 February 2024 (14:24:57 CET)

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Preprint REVIEW | doi:10.20944/preprints202401.0789.v1

Microbiome Modeling: A Beginner’s Guide

Emanuel Lange, Lena Kranert, Jacob Krüger, Dirk Benndorf, Robert Heyer

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: systems microbiology; microbial ecology; omics data integration; metaproteomics; genome-scale modeling; constraint-based modeling; boolean modeling, bioinformatics

Online: 10 January 2024 (09:57:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0981.v1

Tentaclins – a Novel Family of Phage Receptor-Binding Proteins That Can Be Hypermutated by DGR Systems

Ivan K. Baykov, Artem Y. Tikunov, Igor V. Babkin, Valeria A. Fedorets, Elena V. Zhirakovskaia, Nina V. Tikunova

Subject: Biology And Life Sciences, Virology Keywords: Bacteriophage; Genome sequence; Diversity-generating retroelement; C-type lectin; Tentaclin; Adhesin; Ig-like domain; Receptor-binding protein

Online: 15 November 2023 (09:55:37 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0047.v1

Mark Burgin’s Legacy: The General Theory of Information, The Digital Genome, and the Future of Machine Intelligence

Rao Mikkilineni

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: digital genome; general theory of information; structural machines; machine intelligence; knowledge structures; cognizing oracles; super-symbolic computing

Online: 1 November 2023 (10:08:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.0299.v1

Comparative Genomic Analysis Reveals Emergence of ST-231 and ST-395 Klebsiella pneumoniae Strains Associated with High Transmissibility of blaKPC Plasmids

Muna ALMuzahmi, Meher Rizvi, Manawr AL-Quraini, Zakariya AL-Muharrami, Zaaima AL-Jabri

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)

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Preprint REVIEW | doi:10.20944/preprints202307.1110.v1

Next Generation Sequencing in Diagnosis of Multiple Myeloma

Ikram El Fazazi, Hajar Ihlal, Meriame Abbassi, Mohamed Ahakoud, Samira Nmer, Laila Bouguenouch, Rhizlane Berrady, Karim Ouldim, Mohammed El-Azami El-Idrissi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: multiple myeloma; next generation sequencing; whole genome sequencing; whole exome se-quencing; myTYPE panel; minimal residual disease.

Online: 17 July 2023 (15:06:14 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202112.0040.v1

The Comparative Analysis of the DNA Repeat Composition among Cannabis Sativa L., Humulus Lupulus L. And Humulus Japonicus Siebold & Zucc. With Heteromorphic Sex Chromosomes

Julia V. Bocharkina, Oleg S. Alexandrov, Olga V. Razumova, Gennady I. Karlov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Cannabis sativa L.; Humulus lupulus L.; Humulus japonicus Siebold & Zucc.; sex chromosomes; DNA repeats; transposons; genome sequencing

Online: 3 December 2021 (09:25:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0176.v1

Mobile Colistin Resistance Genetic Determinants of Non-typhoid Salmonella enterica Isolates from Russia

K. V. Kuleshov, A. S. Pavlova, E. D. Shedko, Y. V. Mikhaylova, G. Margos, S. Hepner, I. V. Chebotar, E. V. Korneenko, A. T. Podkolzin, V. G. Akimkin

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: whole genome sequencing; antibiotic resistance; Salmonella Enteritidis; Salmonella Typhimurium; Salmonella Bovismorbificans; colistin resistance; mcr-1; mcr-9

Online: 9 November 2021 (13:46:05 CET)

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Preprint REVIEW | doi:10.20944/preprints202104.0602.v2

Biochemistry, Not Oncogenes, may Demystify and Defeat Cancer

Jay Kulsh

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: cancer; DNA sequencing; DNA synthesis; enzyme; free-radicals; genome; HPV; oncogenes; retinoblastoma; ribonucleotide reductase; RnR; SMT; TCGA

Online: 6 July 2021 (11:32:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0094.v1

Chloroplast Genome of Phyllanthus Emblica and Leptopus Cordifolius: Comparative Analysis and Phylogenetic within Family Phyllanthaceae

Umar Rehman, Nighat Sultana, Abdullah ., Abbas Jamal, Maryam Muzaffar, Peter Poczai

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)

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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.

Preprint BRIEF REPORT | doi:10.20944/preprints202105.0526.v1

Circulating SARS-CoV-2 Variants in Italy, October 2020-March 2021

Alessia Lai, Annalisa Bergna, Stefano Menzo, Gianguglielmo Zehender, Sara Caucci, Valeria Ghisetti, Francesca Rizzo, Fabrizio Maggi, Francesco Cerutti, Giorgio Giurato, Alessandro Weisz, Chiara Turchi, Bianca Bruzzone, Francesca Ceccherini-Silberstein, Nicola Clementi, Annapaola Callegaro, Fabio Sagradi, Daniela Francisci, Emmanuele Venanzi Rullo, Ilaria Vicenti, Massimo Clementi, Massimo Galli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 virus; complete genome sequencing; COVID-19 RT-PCR testing; Spike protein; vi-ral variants

Online: 21 May 2021 (15:12:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0273.v1

Integrated into Environmental Biofilm Chromobacterium Vaccinii Survives Winter with Support of Bacterial Community

Daria A. Egorova, Olga L. Voronina, Andrey I. Solovyev, Marina S. Kunda, Ekaterina I. Aksenova, Natalia N. Ryzhova, Ksenya V. Danilova, Valentina S. Rykova, Anastasya A. Scherbakova, Andrey N. Semenov, Nikita B. Polyakov, Daniil A. Grumov, Natalia V. Shevlyagina, Inna V. Dolzhikova, Yulia M. Romanova, Alexander L. Gintsburg

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Chromobacterium vaccinii; biofilm; sharing goods; social cheater; bog microbiome; bacterial genome, violacein, cold adaptation, IDBac, QS mutant

Online: 12 September 2020 (12:04:38 CEST)

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Preprint REVIEW | doi:10.20944/preprints201811.0269.v1

Non-Clonal Chromosome Aberrations and Genome Chaos in Somatic And Germ Cells from Patients and Survivors of Hodgkin Lymphoma, Induced by Anticancer Treatment

Sara Frias, Sandra Ramos, Consuelo Salas, Bertha Molina, Silvia Sánchez-Sandoval, Roberto Rivera-Luna

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: chromosome instability (CIN); chromoplexy; genome chaos; chromosomal heterogeneity; karyotype heterogeneity; non-clonal chromosome aberration (NCCA); second cancer

Online: 12 November 2018 (06:38:41 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.1981.v1

Exploring SVA Insertion Polymorphisms in Shaping Differential Gene Expression in the Central Nervous System

Lauren S Hughes, Alexander Fröhlich, Abigail L Pfaff, Vivien J Bubb, John P Quinn, Sulev Kõks

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SINE-VNTR-Alu; transposable elements; whole genome sequencing; RNA-seq; quantitative trait loci; Amyotrophic Lateral Sclerosis; HLA; MAPT

Online: 26 December 2023 (11:27:43 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.0587.v1

Genomic Characterization of Listeria innocua Isolates Recovered from Cattle Farms, Beef Abattoirs, and Retail Outlets in Gauteng Province, South Africa

James Gana, Nomakorinte Gcebe, Rian Pierneef, Yi Chen, Rebome Moerane, Abiodun Adewale Adesiyun

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: beef production chain; Listeria innocua; whole-genome sequencing; sequence type; an-timicrobial resistance genes; virulence gene; South Africa

Online: 10 July 2023 (09:48:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0480.v1

An Evaluation of Avian Influenza Virus Whole Genome Sequencing Approaches Using Nanopore Technology

Hon S. Ip, Sarah Uhm, Mary Lea Killian, Mia K. Torchetti

Subject: Biology And Life Sciences, Virology Keywords: avian influenza; highly pathogenic avian influenza; next generation sequencing; whole genome sequencing; nanopore technology; methods comparison; clinical validation

Online: 26 January 2023 (15:19:53 CET)

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