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Preprint ARTICLE | doi:10.20944/preprints202208.0175.v1

Ethnobotany Survey of Plants used as Biopesticides by Indigenous People of Plateau State, Nigeria

Ahmed Ali, Lydia Doosuur Ior, Goni Abraham Dogo, John Israila Joshua, John Stephen Gushit

Subject: Biology, Plant Sciences Keywords: biopesticides, ethnobotany; survey; indigenous people; Nigeria

Online: 9 August 2022 (06:11:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0026.v1

Stochastic Inoculum, Biotic Filtering and Species Specific Transmission Shape the Rare Microbiome of Plants

David Johnston-Monje, Janneth P. Gutiérrez, Luis Augusto Becerra Lopez-Lavalle

Subject: Biology, Plant Sciences Keywords: rhizosphere; phyllosphere; endophyte; plant microbiome; plant mycobiome; rare microbiome; fungi; bacteria; microbes; soil microbiology; inoculum; microbial ecology

Online: 1 August 2022 (15:22:30 CEST)

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A plant’s health and productivity is influenced by its associated microbes. Although the common microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (eg. specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum, and pea. Plants were grown inside sealed jars on sterile sand or field soil. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon, however judging by read abundance, up to half of the mycobiome consists of uncommon fungal cells, while less than 11% of bacterial endophytes are rare. Uncommon seed transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes that most heavily colonized shoots, to a lesser extent roots and least of all rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon seed transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant-microbe associations were observed such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.

Preprint REVIEW | doi:10.20944/preprints202207.0404.v1

Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses

Mohd Fadhli Hamdan, Chou Khai Soong Karlson, Ee Yang Teoh, Su-Ee Lau, Boon Chin Tan

Subject: Biology, Plant Sciences Keywords: Abiotic stress; biotic stress; biotechnology; climate change; CRISPR; crop improvement; genome editing

Online: 26 July 2022 (10:44:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0387.v1

Artocarpus Camansi Blanco: A Review on Its Traditional Use, Nutritional Value, Phytochemistry, and Pharmacology

Patrick Joel Bicaldo

Subject: Biology, Plant Sciences Keywords: Artocarpus; Artocarpus camansi; kamansi; phytochemistry; pharmacology; secondary metabolites

Online: 26 July 2022 (05:52:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0334.v1

Computational Biology and Machine Learning Approaches to Identify the Rubber Tree (Hevea brasiliensis L.) Genome Encoded Potential MicroRNAs Targeting Rubber Tree Virus 1

Muhammad Aleem Ashraf, Hafiza Kashaf Tariq, Jallat Khan, Han Cheng

Subject: Biology, Plant Sciences Keywords: Rubber tree capillovirus 1; microRNAs; plant-virus interaction; RNAi: computational algorithms; gene silencing, minimum free energy

Online: 22 July 2022 (09:52:38 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0309.v1

The Role of E3 Ubiquitin Ligases in Chloroplast Function

Katherine A Hand, Nitzan Shabek

Subject: Biology, Plant Sciences Keywords: ubiquitin; E3 ligase; chloroplast; stress; photosynthesis; homeostasis; enzymes

Online: 21 July 2022 (03:20:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0293.v1

Nutrients Composition Changes in Leaves of Quercus leucotrichophora from Different Seasons and Altitudes in the North-West Himalaya

Shalini Sharma, Sunil Puri

Subject: Biology, Plant Sciences Keywords: altitudinal variation; nutrient composition; Quercus leucotrichophora; seasonal variation

Online: 20 July 2022 (05:12:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0143.v1

Quantifying the Influence of Pollen Ageing on the Adhesive Properties of Hypochaeris Radicata Pollen

Steven Huth, Lisa-Maricia Schwarz, Stanislav N. Gorb

Subject: Biology, Plant Sciences Keywords: pollination; pollen adhesion; pollenkitt; atomic force microscopy; cryogenic scanning electron microscopy; centrifugation

Online: 10 July 2022 (05:57:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0047.v1

Hot Water Treatment as Effort to Inhibits The Anthracnose Disease and Maintain The Quality of Situbondo Mango Fruit

Slamet Fauzi, Dodo Brilliant Priyananda, Zidna Amalia Firdausy, Naning Tyas Anggraini, Nuril Azizah

Subject: Biology, Plant Sciences Keywords: Situbondo Mango Fruit; Hot Water Treatment; Anthracnos disease

Online: 4 July 2022 (09:45:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0401.v1

Assessing Loss of Regulatory Divergence, Genome–Transcriptome Incongruence, and Preferential Expression Switching in Abaca/ Banana Backcrosses

Nelzo C. Ereful, Antonio G. Lalusin, Antonio C. Laurena

Subject: Biology, Plant Sciences Keywords: abaca (Musa textilis); allelic imbalance; regulatory divergence; banana (M. balbisiana); allele-specific expression

Online: 29 June 2022 (09:34:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0278.v1

Genome-Wide Identification, and Molecular Evolution of The Magnesium Transporter (MGT) Gene Family in Citrullus Lanatus and Cucumis Sativus

Parviz Heidari, Fatemeh Puresmaeli, Freddy Mora-Poblete

Subject: Biology, Plant Sciences Keywords: Magnesium; Evolution analysis; Plant gene families; Gene sequence analysis; Stresses

Online: 21 June 2022 (03:47:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0090.v1

Ecotype Division and Chemical Diversity of Cynomorium songaricum from Different Geographical Regions

Xinke Zhang, Xiao Sun, Yujing Miao, Min Zhang, Lixia Tian, Chang Liu, Linfang Huang

Subject: Biology, Plant Sciences Keywords: Cynomorium songaricum; ecotype division; chemical diversity; metabolomics

Online: 7 June 2022 (02:54:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0089.v1

The Test of the Availability Hypothesis Across a Protected Area Reveals the Needs for Ex-situ Conservation to Open Window for Ethnobotanical Knowledge Development

Kowiyou Yessoufou, Isidore Muleba, Isaac Tebogo Rampedi

Subject: Biology, Plant Sciences Keywords: Availability hypothesis; Ethnobotany; Ex-situ Conservation; Kruger National Park; Sustainable Development of Traditional Knowledge; Traditional medicine

Online: 6 June 2022 (13:19:18 CEST)

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In ethnobotany, the availability hypothesis predicts that plants that are abundant and easily accessible to people are more likely to be medicinal than not. By protecting species diversity away from people, protected areas (PAs) may act as a limiting factor to a sustainable development of traditional knowledge concerning medicinal uses, and in so doing, PAs provide opportunity to prioritize ex-situ conservation for species that are PAs restricted. In this scenario, ex-situ conservation becomes the only chance for people to develop traditional knowledge on plants which otherwise wouldn’t be documented as traditionally useful to people. To test these expectations, we used data collected for almost 20 years of fieldworks on plant medicinal uses and their abundance inside and outside the Kruger National Park (KNP), South Africa. We fitted four different scenarios of structural equation models (SEMs) to the data collected. We found that total plant abundance (abundance outside + inside KNP) is a significant positive predictor of medicinal status, and so is abundance outside KNP, thus supporting the availability hypothesis. However, not only abundance inside KNP is not a direct significant correlate of medicinal status, but also the relationship between both is negative. The lack of predictive power of inside-abundance is most likely because some species are exclusively found inside KNP, and local communities do not have access to them. It also shows that the positive and direct correlation of total abundance with medicinal status is driven by outside-abundance. In addition, the negative relationships between inside abundance and medicinal status implies that abundant plants inside KNP tend to be not-medicinal, further providing evidence that PAs hinder the development of medicinal knowledge. Furthermore, when inside and outside abundance were included simultaneously in a model as two distinct variables, inside abundance was never a direct significant predictor of medicinal status, but it was so, via an indirect path mediated by outside abundance. This suggests that outside abundance is the key variable driving the development of medicinal plant knowledge. Cumulatively, our findings suggest that anything that promotes the growth of PA-restricted plants beyond the natural realized niches of these plants (ex-situ conservation) such as in botanical gardens, private gardens, in agroforestry systems, etc., is to be promoted so that people-plant interactions may continue for the benefits of ethnobotanical knowledge development.

Preprint ARTICLE | doi:10.20944/preprints202205.0407.v1

Transcriptome Analysis of Fusarium-Tomato Interaction Based on an Up-Dated Genome Annotation of Fusarium Oxysporum F. Sp. Lycopersici Identifies Novel Effector Candidates that Suppress or Induce Cell Death in Nicotiana Benthamiana

Xizhe Sun, Xiangling Fang, Dongmei Wang, David A. Jones, Lisong Ma

Subject: Biology, Plant Sciences Keywords: Fusarium; tomato; novel effector candidates; cell death; Nicotiana benthamiana

Online: 31 May 2022 (03:20:05 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202203.0104.v3

High Atmospheric CO₂ Concentration Causes Increased Respiration by the Oxidative Pentose Phosphate Pathway in Chloroplasts

Thomas Wieloch

Subject: Biology, Plant Sciences Keywords: Calvin-Benson cycle; carbon metabolism; CO2 fertilisation; glucose-6-phosphate shunt; hydrogen stable isotopes; oxidative pentose phosphate pathway; photosynthesis; respiration

Online: 16 May 2022 (12:14:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0208.v1

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Luo Yong Jian, Ru Wang, Li Qing, Song Quan Song, Jun Liu, Zhi Jun Deng

Subject: Biology, Plant Sciences Keywords: RSCU; ENc-GC3s plot; synonymous codon usage bias; Cycas; CAI

Online: 16 May 2022 (12:12:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0096.v1

Particle-based Imaging Tools Revealing Water Flows in Maize Nodal Vascular Plexus

Ulyana S. Zubairova, Aleksandra Yu. Kravtsova, Aleksandr V. Romashchenko, Anastasiia A. Pushkareva, Alexey V. Doroshkov

Subject: Biology, Plant Sciences Keywords: plant 3D imaging; Zea mays L.; vascular system; internodes; nodal plexus; contrast-enhanced magnetic resonance imaging; laser scanning microscopy; lab-on-a-chip; particle image velocimetry; systems biology

Online: 9 May 2022 (03:22:20 CEST)

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Preprint REVIEW | doi:10.20944/preprints202205.0041.v1

Phytochemical and Biological Aspects of Zephyranthes citrina Baker: A Mini-Review

Indrani Biswas, Dipak Paul

Subject: Biology, Plant Sciences Keywords: Amaryllidaceae alkaloids; Biological activities; Traditional medicines; Yellow rain lily; Zephyranthes citrine

Online: 5 May 2022 (12:41:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0036.v1

An Improved Procedure for Agrobacterium-Mediated Transformation of Citrus

Yanjun Li, Dan Tang, Zongrang Liu, Jianjun Chen, Baoping Cheng, Yi Li

Subject: Biology, Plant Sciences Keywords: Citrus; Agrobacterium tumefaciens; transformation efficiency; treatments of Agrobacterium and explants

Online: 5 May 2022 (12:01:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0282.v1

Preparation of a Bacterium Inoculum and Its Evaluation by Analysing Various Characteristics of Compost

Ayesha Ameen, Neelma Munir, Imran Altaf, Rasheeda Bashir, Shagufta Naz, Neha Asghar, Athar Hussain

Subject: Biology, Plant Sciences Keywords: bacteria; compost; organic waste; decomposition; inoculum

Online: 28 April 2022 (10:26:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0281.v1

Diversity of Herbicide-resistance Mechanisms of Avena fatua L. to ACCase-inhibiting Herbicides in the Bajio, Mexico

Antonio Tafoya-Razo, Saúl Alonso Mora-Munguía, Jesús R. Torres-García

Subject: Biology, Plant Sciences Keywords: microevolution; adaptation; ecometabolomics; ACCase-inhibiting herbicides

Online: 28 April 2022 (10:23:01 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202203.0104.v2

Increased Respiration by the Oxidative Pentose Phosphate Pathway in Chloroplasts at High Atmospheric CO₂ Concentration

Thomas Wieloch

Subject: Biology, Plant Sciences Keywords: Calvin-Benson cycle; carbon metabolism; CO2 fertilisation; glucose-6-phosphate shunt; hydrogen stable isotopes; oxidative pentose phosphate pathway; photosynthesis; respiration

Online: 26 April 2022 (09:49:53 CEST)

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Preprint REVIEW | doi:10.20944/preprints202204.0097.v1

Post-proline Cleaving Enzymes (PPCEs): Classification, Structure, Molecular Properties, and Applications

Anis Baharin, Tiew-Yik Ting, Hoe-Han Goh

Subject: Biology, Plant Sciences Keywords: Prolyl endoprotease; prolyl oligopeptidase; protease; protein engineering; proteolytic enzyme; proteomics; therapeutics

Online: 11 April 2022 (11:21:44 CEST)

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Preprint REVIEW | doi:10.20944/preprints202203.0124.v2

Biochemistry and Molecular Basis of Intracellular Flavonoid Transport in Plants

Boas Pucker, Dirk Selmar

Subject: Biology, Plant Sciences Keywords: anthocyanins; proanthocyanidins; flavonols; flavones; flavonoid transport; flavonoid biosynthesis; flavonoid accumulation; ligandin; MATE; ABCC

Online: 28 March 2022 (17:03:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0174.v1

Bioaugmentation Improves Phytoprotection in Halimione Portulacoides Exposed to Mild Salt Stress: Perspectives for Salinized Soil Restoration

João Carreiras, Isabel Caçador, Bernardo Duarte

Subject: Biology, Plant Sciences Keywords: halophyte; rhizobacteria; PGPR; root inoculation; osmotic stress

Online: 14 March 2022 (06:53:44 CET)

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Preprint REVIEW | doi:10.20944/preprints202203.0124.v1

Biochemistry and Molecular Basis of Intracellular Flavonoid Transport in Plants

Boas Pucker, Dirk Selmar

Subject: Biology, Plant Sciences Keywords: anthocyanins; proanthocyanidins; flavonols; flavones; flavonoid transport; flavonoid biosynthesis; flavonoid accumulation; ligandin; MATE; ABCC

Online: 8 March 2022 (13:15:22 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202203.0104.v1

Respiration by the Oxidative Pentose Phosphate Pathway in Chloroplasts Responds to Atmospheric CO₂ Concentration

Thomas Wieloch

Subject: Biology, Plant Sciences Keywords: Calvin-Benson cycle; carbon metabolism; CO2 fertilisation; glucose-6-phosphate shunt; hydrogen stable isotopes; oxidative pentose phosphate pathway; photosynthesis; respiration

Online: 7 March 2022 (14:50:43 CET)

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Preprint REVIEW | doi:10.20944/preprints202203.0103.v1

Intertwined Roles of Reactive Oxygen Species and Salicylic Acid Signaling Are Crucial for the Plant Response to Biotic Stress

Tjaša Lukan, Anna Coll

Subject: Biology, Plant Sciences Keywords: plant immune response; reactive oxygen species; salicylic acid; reactive oxygen species-salicylic acid crosstalk; programmed cell death; hypersensitive response-conferred resistance; RBOH NADPH oxidases; chloroplastic redox state; biosensors; precision transcriptomics

Online: 7 March 2022 (14:46:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202203.0084.v1

Long-Term Tree Survival and Diversity of Highway Tree Planting Projects

Allyson B. Salisbury, Jason W. Miesbauer, Andrew K. Koeser

Subject: Biology, Plant Sciences Keywords: drought tolerance; roadside woody vegetation; Simpson diversity; site conditions; tree mortality; tree planting initiatives

Online: 4 March 2022 (17:04:27 CET)

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Preprint ARTICLE | doi:10.20944/preprints202203.0082.v1

Seed Priming Enhances Seed Germination and Morphological Traits of Lactuca Sativa L. Under Salt Stress

Bikash Adhikari, Omolayo Joshua Olorunwa, T. Casey Barickman

Subject: Biology, Plant Sciences Keywords: Hydro-priming; lettuce; Sodium chloride; synchronization; electrolyte leakage

Online: 4 March 2022 (13:44:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202203.0049.v1

Evolutionary and Functional Characterization of Cytochrome P450 in Cotton Reveal the Role of Subgenome Expression of GhCYP78A for Cotton Fiber Initiation

Priti Prasad, Rishi Kumar Verma, Uzma Khatoon, Samir V. Sawant, Sumit K. Bag

Subject: Biology, Plant Sciences Keywords: Cotton; Fiber initiation; Cell differentiation; CYP78A; Endoreduplication; Biomass

Online: 2 March 2022 (12:32:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0295.v1

Genome-Wide Identification and Expression Analysis of bZIP Transcription Factors under Abiotic Stress in Alfalfa (Medicago sativa L.)

Atit Parajuli, Karen Sanguinet, Zhiwu Zhang

Subject: Biology, Plant Sciences Keywords: Alfalfa; bZIP transcription factor; phylogenetic analysis; expression pattern; abiotic stress

Online: 23 February 2022 (13:40:34 CET)

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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 physico-chemical 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. 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.

Preprint REVIEW | doi:10.20944/preprints202202.0174.v1

Root Tragedy of the Commons: What is it and Where Might it Occur?

Ciro Cabal

Subject: Biology, Plant Sciences Keywords: Game theory; Plant behavioral ecology; Plant competition; Plant interaction mechanisms; Root foraging strategies; Root methods

Online: 14 February 2022 (11:29:43 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0113.v1

Delineating the Tissue-Mediated Drought Stress Governed Tuning of Conserved miR408 and Its Targets in Rice

Sonia Balyan, Shivani Kansal, Ringyao Jajo, Pratyush Rajiv Behere, Rishika Chatterjee, Saurabh Raghuvanshi

Subject: Biology, Plant Sciences Keywords: miR408; conserved; drought; N22; miRNA target

Online: 8 February 2022 (13:17:14 CET)

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MicroRNAs act as the cardinal post-transcriptional monitors of gene regulatory networks sculpturing the developmental plasticity and stress responses in plants. Single miRNA target several genes and how the transcriptional regulation of miRNA impacts its pool of targets in different tissues and stress conditions is still elusive. The present study investigated the highly conserved and evolving MIR408 family comprehensively by redefining its evolutionary conservation and diversification in plants followed by detailed functional analysis in rice. MIR408 family comprises three dominant mature forms (21 nt) including a distinct monocot variant. Plant MIR408 family can be divided into six groups. miR408 majorly cleave genes belonging to blue copper protein in addition to several other species-specific targets in plants. Screening of 4726 rice accessions identified 22 sequence variants in 1 Kb upstream (15) and MIR408 region leading to the identification of 8 haplotypes (3: Japonica-specific and 5: Indica-specific). miR408-3p follows flag leaf preferential and drought upregulated expression profile in flag leaf and roots of N22 which seems to be regulated by differential fraction of mCs in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice. Twelve high confidence targets including 4 plantacyanins (OsUCL6, 7, 9 and 30), pirin, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine rich cell wall, deoxyuridine 5-triphosphate nucleotidohydrolaseand OsERF7 with antagonistic expression under most conditions. Further, over-expression of osa-MIR408 in drought sensitive rice cultivar leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced the dehydration stress tolerance at seedling stage.

Preprint ARTICLE | doi:10.20944/preprints202202.0072.v1

The Endemic Vascular Flora of Sardinia: a Dynamic Checklist with an Overview of Biogeography and Conservation Status

Mauro Fois, Emmanuele Farris, Giacomo Calvia, Giuliano Campus, Giuseppe Fenu, Marco Porceddu, Gianluigi Bacchetta

Subject: Biology, Plant Sciences Keywords: Mediterranean flora; endemic plants; IUCN assessments; island biogeography; plant conservation; Tyrrhenian islands; biological forms; plant evolution and distribution; plant diversity

Online: 4 February 2022 (12:06:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0437.v1

Growth, Phycobiliproteins, Chlorophyll and Carotenoids Content of the Marine Cyanobacteria Phormidium sp. And Cyanothece sp. As Affected by White and Colored Artificial Light in Batch Cultures

George N. Hotos, Theodoros I. Antoniadis

Subject: Biology, Plant Sciences Keywords: cyanobacteria; Phormidium; Cyanothece; culture growth; light; chlorophyll; carotenoids; phycocyanin; phycoerythrin; allophycocyanin; phycobiliproteins

Online: 28 January 2022 (12:21:12 CET)

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Preprint REVIEW | doi:10.20944/preprints202201.0310.v1

DNA Barcoding in Plants and Animals: A Critical Review

Sheikh Sunzid Ahmed

Subject: Biology, Plant Sciences Keywords: DNA barcoding; metabarcoding; BOLD; taxonomy; biodiversity; molecular marker.

Online: 20 January 2022 (15:15:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0211.v1

The Spermidine Synthase Gene SPD1: A Novel Auxotrophic Marker for Chlamydomonas Reinhardtii Designed by Enhanced CRISPR/Cas9 Gene Editing

Robert A. Freudenberg, Luisa Wittemeier, Alexander Einhaus, Thomas Baier, Olaf Kruse

Subject: Biology, Plant Sciences Keywords: microalgae; CRISPR/Cas9; gene editing; spermidine; SPD1; auxotrophy; selectable marker

Online: 14 January 2022 (11:55:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0113.v1

MISF2 Encodes an Essential Mitochondrial Splicing Co-factor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana

Tan-Trung Nguyen, Corinne Best, Sofia Shevtsov, Michal Zmudjak, Martine Quadrado, Ron Mizrahi, Hagit Zer, Hakim Mireau, Oren Ostersetzer-Biran

Subject: Biology, Plant Sciences Keywords: Group II; Intron; Splicing; PPR; Respiration; Complex I; Mitochondria; Embryogenesis; Arabidopsis; Angiosperms.

Online: 10 January 2022 (12:46:06 CET)

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Preprint REVIEW | doi:10.20944/preprints202112.0523.v1

The Avocado (Persea americana Mill.): A Review and Sustainability Perspectives

Subhash Janardhan Bhore, Daniela Salgado Ochoa, Amina Al Houssari, Angela Lopez Zelaya, Ru Yang, Zixin Chen, Sarah Siddiqui Deeya, Sheila C. da Silva Sens, Margherita Schumann, Zihan Zhang, Eslam Eltantawy

Subject: Biology, Plant Sciences Keywords: Agriculture; antioxidants; Avocado; Cameroon; CAMAAY; deforestation; environment; food security; green gold; health; one health; sustainable development goals (SDGs); sustainability

Online: 31 December 2021 (13:47:40 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0509.v1

Development and Validation of a One-Step Reverse Transcription Real-Time PCR Assay for Simultaneous Detection and Identification of Tomato Mottle Mosaic Virus and Tomato Brown Rugose Fruit Virus

Antonio Tiberini, Ariana Manglli, Anna Taglienti, Ana Vučurović, Jakob Brodaric, Luca Ferretti, Marta Luigi, Andrea Gentili, Nataša Mehle

Subject: Biology, Plant Sciences Keywords: ToBRFV; ToMMV; Solanum lycopersicum; Capsicum annum; leaves detection; seeds detections; performance criteria

Online: 31 December 2021 (11:12:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0480.v1

Herzog Vindicated: Integrative Taxonomy Reveals that Trichostomum brachydontium (Pottiaceae, Bryophyta) Comprises Several Species

Rosa M. Ros, Olaf Werner, Ron D. Porley

Subject: Biology, Plant Sciences Keywords: cp-rbcL; nr-ITS region; biodiversity; distribution; Mediterranean-Atlantic Europe; mosses; nomenclature; taxonomy; Trichostomum herzogii nom. nov.; Trichostomum meridionale sp. nov.

Online: 30 December 2021 (08:58:49 CET)

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Preprint ARTICLE | doi:10.20944/preprints202101.0320.v2

Phylogenetic and Expression Analysis of CENH3 and APOLLO Genes in Sexual and Apomictic Boechera Species

Evgeny Bakin, Fatih Sezer, Aslıhan Özbilen, Irem Kilic, Buket Uner, Mike Rayko, Kemal Melih Taskin, Vladimir Brukhin

Subject: Biology, Plant Sciences Keywords: Boechera; Brassicaceae; CENH3; APOLLO; apomixis associated genes; cell division; apomeiosis

Online: 20 December 2021 (10:40:57 CET)

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Apomictic plants (reproducing via asexual seeds), unlike sexual individuals, avoid meiosis and egg cell fertilization. Consequently, apomixis is very important for fixing maternal genotypes in the next plant generations. Despite the progress in the study of apomixis, molecular and genetic regulation of the latter remains poorly understood. So far APOLLO (Aspartate Glutamate Aspartate Aspartate histidine exonuclease) is one of the very few described genes associated with apomixis in Boechera species. The centromere-specific histone H3 variant encoded by CENH3 gene is essential for cell division. Mutations in CENH3 disrupt chromosome segregation during mitosis and meiosis since the attachment of spindle microtubules to a mutated form of the CENH3 histone fails. This paper presents in silico characteristic of APOLLO and CENH3 genes, which may affect apomixis. Also, we characterize the structure of CENH3, study expression levels of APOLLO and CENH3 in gynoecium/siliques of the natural diploid apomictic and sexual Boechera species at the stages of before and after fertilization. While CENH3 was a single copy gene in all Boechera species, the APOLLO gene have several polymorphic alleles associated with sexual and apomictic reproduction in the Boechera genera. Expression of the APOLLO apo-allele during meiosis was upregulated in gynoecium of apomict B. divaricarpa downregulating after meiosis until 4th day after pollination (DAP). On the 5th DAP, expression in apomictic siliques increased again. In sexual B. stricta gynoecium and siliques APOLLO apo-allele did not express. Expression of the APOLLO sex-allele during and after meiosis in gynoecium of sexual plants was several times higher than that in apomictic gynoecium. However, after pollination the sex-allele was downregulated in sexual siliques to the level of apomicts and increased sharply on the 5th DAP, while in apomictic siliques it almost did not express. At the meiotic stage, the expression level of CENH3 in the gynoecium of apomicts was two times lower than that of the sexual Boechera, decreasing in both species after meiosis and keep remaining very low in siliques of both species for several days after artificial pollination until the 4th DAP, when the expression level raised in sexual B. stricta siliques exceeding 5 times the level in apomictic B. divaricarpa siliques. We also discuss polymorphism and phylogeny of the APOLLO and CENH3 genes.

Preprint ARTICLE | doi:10.20944/preprints202112.0111.v1

Transcriptomic and Physiological Response of Durum Wheat Grain to Short-Term Heat Stress during Early Grain Filling

Anita Arenas-M, Francisca M. Castillo, Diego Godoy, Javier Canales, Daniel F. Calderini

Subject: Biology, Plant Sciences Keywords: Durum wheat; heat stress; grain weight; grain quality; RNA-seq; gene regulatory network; DOF transcription factor

Online: 7 December 2021 (23:38:32 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0089.v1

Exploring the Efficacy of Aqueous Extracts of Malus domestica var Anna, Prunus persica, Ricinus Communis and Carica papaya Against Pathogenic Bacterial Strains

Malini Bhattacharyya, Sudeep Semwal, Jyoti Thapliyal, Babita Patni

Subject: Biology, Plant Sciences Keywords: Antimicrobial activities; Medicinal plants; Herbal medicines; WHO

Online: 6 December 2021 (15:40:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0071.v1

Genome Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection

Juan Camilo Alvarez-Diaz, Manon Richard, Vincent Thareau, Gianluca Teano, Christine Paysant-Le-Roux, Guillem Rigaill, Stéphanie Pflieger, Ariane Gratias, Valérie Geffroy

Subject: Biology, Plant Sciences Keywords: Phaseolus vulgaris; Colletotrichum lindemuthianum; RNA silencing; Argonaute; double-stranded RNA binding (DRB); RNA-dependent RNA polymerase (RDR); Pol IV

Online: 6 December 2021 (12:42:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0565.v1

Expression of Genes Related to Plant Hormone Signal Transduction in Jerusalem artichoke (Helianthus tuberosus L.) Seedlings Under Salt Stress

Yue Yang, Wang Jueyun, Ren Wencai, Zhaosheng Zhou, Long Xiaohua, Gao Xiumei, Zed Rengel

Subject: Biology, Plant Sciences Keywords: Salt stress; Jerusalem artichoke; Time series analysis; RNA-seq

Online: 30 November 2021 (11:55:51 CET)

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Background: Jerusalem artichoke (Helianthus tuberosus L.) is tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, the plant physiology, biochemistry and gene transcription are likely to undergo large changes. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h, 6 h, 12 h, 24 h and 48 h, with 150,129 unigenes and 9023 DEGs (Differentially Expressed Genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among the groups convergence. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belongs to PYL (abscisic acid receptor PYR / PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (Genes such as jasmonate ZIM-domain gene) and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qPCR of 12 randomly selected genes confirmed the accuracy of RNA-seq. Conclusions: Under the impact of high salinity (300mM) environment, Jerusalem artichoke in the seedling stage was difficult to survive for a long time, and the phenotype was severe in the short term. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern.

Preprint COMMUNICATION | doi:10.20944/preprints202111.0492.v1

A New Taxon of Sideroxylon mascatense in Oman

Eric Hopkins, Rashid Al-Yahyai, Shahina Ghazanfar

Subject: Biology, Plant Sciences Keywords: Sideroxylon mascatense; Oman; Western Hajar Mountains

Online: 26 November 2021 (08:33:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0424.v1

CBM: An IoT Enabled LiDAR Sensor for In-field Crop Height and Biomass Measurements

Bikram Pratap Banerjee, German Spangenberg, Surya Kant

Subject: Biology, Plant Sciences Keywords: Internet of things; Raspberry Pi; LiDAR; GNSS; High-throughput plant phenotyping; Precision agriculture

Online: 23 November 2021 (14:15:26 CET)

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Preprint ARTICLE | doi:10.20944/preprints202109.0256.v3

Seed Biologists Beware: Estimates of Initial Viability Based on Ungerminated Seeds at the End of an Experiment May Be Error-Prone

Byron B. Lamont

Subject: Biology, Plant Sciences Keywords: germination; Leucadendron; seed storage; seed viability estimation; viability loss

Online: 17 November 2021 (13:15:02 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0167.v1

Plastome Diversity and Phylogenomic Relationships in Asteraceae

Joan Pere Pascual-Díaz, Sònia Garcia, Daniel Vitales

Subject: Biology, Plant Sciences Keywords: chloroplast genome; Compositae; phylogenetic incongruence; plastid DNA; Senecioneae

Online: 9 November 2021 (12:51:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0159.v1

Arabidopsis PII Proteins Form Characteristic Foci in Chloroplasts Indicating Novel Properties in Protein Interaction and Degradation

Natalie Krieger, Kai-Florian Pastryk, Karl Forchhammer, Üner Kolukisaoglu

Subject: Biology, Plant Sciences Keywords: plant PII protein; protein-protein interaction; PII foci; BiFC; FRET/FLIM; plastidic protein degradation; cpUPR

Online: 8 November 2021 (15:30:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0129.v1

Root-To-Shoot Signaling for the Coding of Support Thickness in Pea Plants

Silvia Guerra, Bianca Bonato, Qiuran Wang, Alessandro Peressotti, Francesca Peressotti, Walter Baccinelli, Maria Bulgheroni, Umberto Castiello

Subject: Biology, Plant Sciences Keywords: Plant behavior; root-to-shoot-signaling; plants movement; kinematics; climbing plants; circumnutation

Online: 8 November 2021 (11:53:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202109.0256.v2

Seed Biologists Beware: Estimates of Initial Viability Based on Ungerminated Seeds at the End of an Experiment May Be Error-Prone

Byron B. Lamont

Subject: Biology, Plant Sciences Keywords: germination; Leucadendron; seed storage; seed viability estimation; viability loss

Online: 5 November 2021 (14:00:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints202110.0332.v1

iPReditor-CMG: Improving Predictive RNA Editor for Crop Mitochondrial Genomes Using Genomic Sequence Features and Optimal Support Vector Machine

Sidong Qin, Yanjun Fan, Shengnan Hu, Yongqiang Wang, Ziqi Wang, Yixiang Cao, Qiyuan Liu, Siqiao Tan, Zhijun Dai, Wei Zhou

Subject: Biology, Plant Sciences Keywords: iPReditor-CMG; RNA editing site; Mitochondrial genomes; genomic sequence feature; support vector machine

Online: 22 October 2021 (15:11:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202110.0306.v1

Investigation and Computational Analysis of Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights Into Sulfur Adjustment for Proper Development and Stimuli Responses

Sahar Faraji, Parviz Heidari, Hoorieh Amouei, Ertugrul Filiz, Abdullah ., Peter Poczai

Subject: Biology, Plant Sciences Keywords: Sulfur; Sulfotransferase; Potato; Bioinformatics; Proteins structure; Stimuli coping

Online: 21 October 2021 (12:41:52 CEST)

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Preprint REVIEW | doi:10.20944/preprints202110.0305.v1

Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Medicago sativa L.)

Cesar A Medina, Harpreet Kaur, Ian Ray, Long-Xi Yu

Subject: Biology, Plant Sciences Keywords: Genomic selection; WGBLUP; Medicago sativa

Online: 21 October 2021 (12:35:16 CEST)

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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, 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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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, 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/preprints202110.0229.v1

A Cryptic Invader of the Genus Persicaria (Polygonaceae) in La Palma and Gran Canaria (Spain, Canary Islands)

Filip Verloove, Otto Rainer, Steven Janssens, Sang-Tae Kim

Subject: Biology, Plant Sciences Keywords: Canary Islands; cryptic invasion; molecular phylogeny; Persicaria; taxonomy

Online: 15 October 2021 (14:34:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202110.0218.v1

Medieval Forest Dynamics in the Iberian Pyrenees: A Comparison Between Low- and High-mountain Areas

Valentí Rull, Teresa Vegas-Vilarrúbia

Subject: Biology, Plant Sciences Keywords: palynology; Pyrenees; Middle Ages; forest dynamics; forest management; resilience; deforestation; land use; climatic change

Online: 14 October 2021 (13:04:11 CEST)

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This paper compares the Medieval (ca. 400–1500 CE) dynamics of forests from low-mountain (Montcortès; ca. 1000 m a.s.l.) and high-mountain (Sant Maurici; 1900 m a.s.l.) areas of the Iberian Pyrenees, both of which experienced similar climatic forcing but different anthropogenic pressures. The main aim is to identify forest changes over time and associate them with the corresponding climatic and anthropogenic drivers (or synergies among them) to test how different forests at different elevations respond to external forcings. This could be useful to evaluate the hypothesis of general Pyrenean deforestation during the Middle Ages leading to present-day landscapes and to improve the background for forest conservation. The study uses palynological analysis of lake sediments, historical documents and paleoecological reconstructions based on pollen-independent proxies. The two sites studied showed different forest trajectories. The Montcortès area was subjected to intense human pressure during regional deforestation up to a maximum of ca. 1000 CE. Further forest recovery took place until the end of the Middle Ages due to a change in forest management, including the abandonment of slash-and-burn practices. Climatic shifts indirectly influenced forest trends by regulating human migrations and the resulting shifts in the type and intensity of forest exploitation. The highland Sant Maurici forests exhibited a remarkably long-standing constancy and an exceptional resilience to climatic shifts, which were unable to affect forest extension and composition, and to local human pressure, from which they rapidly recovered. The Montcortès and Sant Maurici records did not follow the rule of an irreversible forest clearing during the Middle Ages leading to present-day landscapes. The present Montcortès landscape was shaped after a Medieval forest recovery, a new Modern-Age deforestation and a further forest recovery during the last centuries. The Sant Maurici forests remained apparently untouched since the Bronze Age and were never cleared during the Middle Ages. The relevance of these findings for forest conservation is briefly addressed, and the need for the development of more high-resolution studies on Pyrenean forest dynamics is highlighted.

Preprint REVIEW | doi:10.20944/preprints202110.0060.v3

RNAi Crop Protection Advances

Alejandro Hernández-Soto, Randall Chacón-Cerdas

Subject: Biology, Plant Sciences Keywords: RNAi; dsRNA; silencing; encapsulation; liposomes; virus-like particles; polyplex nanoparticles; bio-clay; regulatory

Online: 13 October 2021 (15:39:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202110.0154.v1

Effects of Irrigation and Fertilization on the Morpho-Physiological Traits of Populus sibirica Hort. Ex Tausch and Ulmus pumila L. In the Semi-arid Steppe Region of Mongolia

Ser-Oddamba Byambadorj, Byung Bae Park, Jonathan O. Hernandez, Enkhchimeg Tsedensodnom, Otgonsaikhan Byambasuren, Antonio Montagnoli, Donato Chiatante, Batkhuu Nyam-Osor

Subject: Biology, Plant Sciences Keywords: arid and semi-arid; afforestation; desertification; drought effects; compost fertilizer

Online: 11 October 2021 (10:49:33 CEST)

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Preprint REVIEW | doi:10.20944/preprints202110.0060.v2

RNAi Crop Protection Advances

Alejandro Hernández-Soto, Randall Chacón-Cerdas

Subject: Biology, Plant Sciences Keywords: RNAi; dsRNA; silencing; encapsulation; liposomes; virus-like particles; polyplex nanoparticles; bio-clay; regulatory

Online: 6 October 2021 (11:48:50 CEST)

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Preprint REVIEW | doi:10.20944/preprints202110.0060.v1

RNAi Crop Protection Advances

Alejandro Hernández-Soto, Randall Chacón-Cerdas

Subject: Biology, Plant Sciences Keywords: RNAi; dsRNA; silencing; encapsulation; liposomes; virus-like particles; polyplex nanoparticles; bio-clay; regulatory

Online: 4 October 2021 (14:20:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0507.v1

Epigenetic Modifications in Plant Development and Reproduction

Vladimir Brukhin, Emidio Albertini

Subject: Biology, Plant Sciences Keywords: epigenetics; plant development; microsporogenesis; megasporogenesis; male and female gametophytes; embryogenesis; endospermogenesis; sexual and asexual reproduction

Online: 30 September 2021 (09:16:17 CEST)

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Plants are exposed to highly fluctuating effects of light, temperature, weather conditions and many other environmental factors throughout their life. As sessile or-ganisms, unlike animals, they are unable to escape, hide or even change their position. Therefore, the growth and development of plants is largely determined by interaction with the external environment, the success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addi-tion to how environmental factors can change the patterns of genes expression, epige-netic regulation determines how genetic expression changes during the differentiation of one cell type into another, and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many 'epigenomes'. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction, when epigenetic marks are eliminated during meiosis and early embry-ogenesis and later reappear. However, during asexual plant reproduction, when meio-sis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adap-tive significance. In asexuals, epigenetic regulation is of particular importance for im-parting plasticity to the phenotype, when the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review. In the last two decades, a lot of data on the epigenetic regulation of plants has appeared, as well as works summarizing the accumulated knowledge (Verhoeven and Preite 2013; Pikaard and Scheid 2014; Gehring 2019; Ono and Kinoshita 2021), nevertheless, many questions remain unclear, and a number of results are contradic-tory. New in this area data is constantly emerging. We tried to take into account and discuss the main findings and conclusions in this field.

Preprint ARTICLE | doi:10.20944/preprints202109.0395.v1

Absorption and Translocation of [14c]2,4-Dichlorophenoxyacetic Scid in Herbicide-tolerant Chromosome Substitution Lines of Gossypium Hirsutum L.

Loida M Perez, Ziming Yue, Sukumar Saha, Jeffrey F. D. Dean, Johnie N Jenkins, David M Stelly, Te Ming Tseng

Subject: Biology, Plant Sciences Keywords: 2,4-D; upland cotton; chromosome substitution lines; herbicide tolerance; 2,4-D absorption and translocation

Online: 23 September 2021 (08:10:50 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0310.v1

Interaction Between Grasses and Epichloe Endophytes and Its Significance to Biotic and Abiotic Stress Tolerance and the Rhi-Zosphere

Kendall Carroll Lee, Ali Missaoui, Kishan Mahmud, Holly Presley, Marin Lonnee

Subject: Biology, Plant Sciences Keywords: endophyte; epichloe; grass; mechanisms; stress

Online: 17 September 2021 (12:08:15 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0309.v1

Trichoderma atroviride LZ42 Releases Volatile Organic Compounds Promoting Plant Growth and Resisting Fusarium wilt Disease in Tomatoes

Hong Jiang, Yuxin Rao, Linzhou Zeng, Li Mei, Yongjun Wang

Subject: Biology, Plant Sciences Keywords: Trichoderma atroviride; volatile organic compounds; tomato; biostimulation; biocontrol; Fusarium wilt disease

Online: 17 September 2021 (12:03:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0256.v1

Seed Biologists Beware: End-of-Trial Estimation of Initial Viability May Be Error-Prone Due to Unexpected Seed Death during the Experiment

Byron B. Lamont, Rosemary J. Newton, Pablo Gomez-Barreiro, Tianhua He

Subject: Biology, Plant Sciences Keywords: germination; Leucadendron; seed storage; seed viability estimation; viability loss

Online: 15 September 2021 (12:19:18 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0153.v1

Microbial Biosurfactant: A New Frontier for Sustainable Agriculture and Pharmaceutical Industries

Ajay Kumar, Sandeep Kumar Singh, Chandra Kant, Hariom Verma, Chandra Kant, Prem Pratap Singh, Arpan Modi, Samir Droby, Mahipal Singh Kesawat, Hemasundar Alavilli, Shashi Kant Bhatia, Ganesh Dattatraya Saratale, Rijuta Ganesh Saratale, Sang-Min Chung, Manu Kumar

Subject: Biology, Plant Sciences Keywords: Biosurfactants; Critical micelle concentration (C.M.C.); Antioxidant; Microorganism; Soil quality; Plant disease management

Online: 8 September 2021 (13:34:43 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0136.v1

A Comprehensive Review of the Nutritional, Pharmacological, and Industrial Value of Polyphenolic Antioxidants Found in Onions

Meenakshi Sharma, Arpitha Bandi

Subject: Biology, Plant Sciences Keywords: onion; polyphenolics; antioxidants; extraction; health

Online: 8 September 2021 (08:48:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0117.v1

Anticandidosic Activity and Acute Toxicity of Quercus suber L. Bark Extracts

Qamar Lahlimi-Alami, Rajaa Layachi, Rachida Hassikou, Jalila Benjelloun, Naima Guennoun, Younes Zaid, Sarah Bouzroud

Subject: Biology, Plant Sciences Keywords: Anticandidosic activity; Candida albicans; Quercus suber L.; Methanolic extracts; Traditional pharmacopoeia; Acute Toxicity

Online: 7 September 2021 (10:32:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0049.v1

Comparison of the Non-Invasive Monitoring of Fresh-Cut Lettuce Condition with Imaging Reflectance Hyperspectrometer and Imaging PAM-Fluorimeter

Boris Shurygin, Olga Chivkunova, Olga Solovchenko, Alexei Solovchenko, Alexey Dorokhov, Igor Smirnov, Dmitriy Khort, Maxim Astashev

Subject: Biology, Plant Sciences Keywords: reflectance; dehydration stress; proximal sensing; vegetation indices; pigments.

Online: 2 September 2021 (16:38:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0571.v1

Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing

Marine Guilcher, Arnaud Liehrmann, Chloé Seyman, Thomas Blein, Guillem Rigaill, Benoit Castandet, Etienne Delannoy

Subject: Biology, Plant Sciences Keywords: Arabidopsis thaliana; plastid; co-maturation; post-transcriptional; Nanopore

Online: 31 August 2021 (11:48:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0497.v1

Close-range Hyperspectral Spectroscopy Reveals Leaf Water Content Dynamics

Samuli Junttila, Teemu Hölttä, Ninni Saarinen, Ville Kankare, Tuomas Yrttimaa, Juha Hyyppä, Mikko Vastaranta

Subject: Biology, Plant Sciences Keywords: leaf water content; hyperspectral spectroscopy; leaf water potential; drought; diurnal cycle; plant water status; relative water content; equivalent water thickness; Dracaena marginate; water stress; leaf water variation

Online: 25 August 2021 (15:00:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0478.v1

Influence of Foliar Application of Glycinebetaine on Tagetes Erecta L Yield Cultivated under Salinity Conditions

Khalid Alamer, Esmat Ali

Subject: Biology, Plant Sciences Keywords: antioxidant activity; chlorophyll; glycinebetaine; membrane stability index; salt stress

Online: 25 August 2021 (08:19:23 CEST)

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Preprint ESSAY | doi:10.20944/preprints202108.0402.v1

Perspective on Sex and Regeneration

Moshe Reuveni

Subject: Biology, Plant Sciences Keywords: Regeneration; asexual propagation; multicellular organisms; wound repair; maturation

Online: 19 August 2021 (11:27:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0381.v1

Genotype-Dependent Variation of Nutritional Quality-Related Traits in Quinoa Seeds

Sara Granado-Rodríguez, Susana Vilariño-Rodríguez, Isaac Maestro-Gaintán, Javier Matías, María José Rodríguez, Patricia Calvo, Verónica Cruz, Luis Bolaños, María Reguera

Subject: Biology, Plant Sciences Keywords: quinoa; genotype; nutritional traits; seed quality

Online: 18 August 2021 (14:00:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0346.v1

Micropropagation of Rare Scutellaria Havanensis Jacq. And Preliminary Studies on Antioxidant Capacity and Anti-cancer Potential

Lani Irvin, Yarelia Zavala Ortiz, Kamila Rivera Rivera, Brajesh Nanda Vaidya, Samantha H Sherman, Juan A Negron Berrios, Nirmal Joshee, Alok Arun

Subject: Biology, Plant Sciences Keywords: Conservation; HCT 116 cells; polyphenol; trichomes

Online: 16 August 2021 (14:50:44 CEST)

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Working Paper ARTICLE

Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines

Sonika Kumar, Ashleigh Ruggles, Sam Logan, Alora Mazarakis, Tyson Thomas, Matthew Bates, Dave Reed, Clayton Grosse, Zhigang Li, Jane Grimwood, Jeremy Schmutz, Christopher A Saski

Subject: Biology, Plant Sciences Keywords: callus; genotype-specific recalcitrance; reprogramming; somatic embryogenesis; transcriptomics; upland cotton

Online: 20 July 2021 (15:30:47 CEST)

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Working Paper ARTICLE

Metabolomics Response to Drought Stress in Morus notabilis variety Yu-711

Michael Ackah, Yisu Shi, Mengmeng Wu, Lei Wang, Guo Peng, Guo Liangliang, Jin Xin, Li Shaocong, Zhang Qiaonan, Changyu Qiu, Qiang Lin, Weiguo Zhao

Subject: Biology, Plant Sciences Keywords: untargeted approach; metabolites; drought stress; mulberry, LC-MS

Online: 6 July 2021 (17:23:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202106.0412.v1

The Crosstalk of Melatonin and Hydrogen Sulfide Determines Photosynthetic Performance by Regulation of Carbohydrate Metabolism in Wheat under Heat Stress

Noushina Iqbal, Mehar Fatma, Harsha Gautam, Shahid Umar, Adriano Sofo, Ilaria D'Ippolito, Nafees A. Khan

Subject: Biology, Plant Sciences Keywords: Carbohydrate; heat stress; hydrogen sulphide; hypotaurine; melatonin

Online: 15 June 2021 (15:21:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0107.v1

Thioredoxins o1 and h2 Show Different Subcellular Localizations and Redox-Active Functions, but Cooperatively Affect NADPH Redox Poise and Photosynthetic Performance in Fluctuating Light

Liang-Yu Hou, Martin Lehmann, Peter Geigenberger

Subject: Biology, Plant Sciences Keywords: Trx o1; Trx h2; metabolomics; ascorbate; glutathione; NAD(P)(H); photosynthetic performance; fluctuating light; Arabidopsis thaliana

Online: 2 March 2021 (16:19:40 CET)

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Preprint REVIEW | doi:10.20944/preprints202102.0466.v1

A Review on Response Mechanism of Plants to Drought Stress

Xinyi Yang, Meiqi Lu, Yvfei Wang, Yiran Wang, Zhijie Liu, Su Chen

Subject: Biology, Plant Sciences Keywords: Drought stress; Osmotic regulation; LEA protein; ROS; Signaling; Drought-responsive gene

Online: 22 February 2021 (12:38:05 CET)

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Preprint REVIEW | doi:10.20944/preprints202102.0033.v1

CRISPR/dCas9-based Systems: Mechanisms and Applications in Plant Sciences

Chou Khai Soong Karlson, Siti Nurfadhlina Mohd Noor, Nadja Nolte, Boon Chin Tan

Subject: Biology, Plant Sciences Keywords: CRISPR interference; CRISPR/dCas9 system; crop improvement; gene silencing; RNAi; transcriptional regulation

Online: 1 February 2021 (13:31:04 CET)

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Preprint REVIEW | doi:10.20944/preprints202101.0616.v1

Plant Nitric Oxide Signaling under Drought Stress

Su-Ee Lau, Mohd Fadhli Hamdan, Teen-Lee Pua, Noor Baity Saidi, Boon Chin Tan

Subject: Biology, Plant Sciences Keywords: abiotic stress; crop improvement; drought; nitric oxide; S-nitrosylation; signaling molecule; water deficit

Online: 29 January 2021 (12:14:53 CET)

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Working Paper ARTICLE

Visual Growth Tracking for Automated Leaf Stage Monitoring based on Image Sequence Analysis

Srinidhi Bashyam, Sruti Das Choudhury, Ashok Samal, Tala Awada

Subject: Biology, Plant Sciences Keywords: Plant architecture determination; graph theoretic approach; leaf detection; leaf tracking; leaf status report.

Online: 22 January 2021 (14:01:50 CET)

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Preprint ARTICLE | doi:10.20944/preprints202101.0204.v1

Chitosan Elicitation Impacts Flavonolignan Biosynthesis in Silybum marianum (L.) Gaertn Cell Suspension and Enhances Antioxidant and Anti-inflammatory Activities of Cell Extracts

Muzamil Shah, Hasnain Jan, Samantha Drouet, Duangjai Tungmunnithum, Jafir Hussain Shirazi, Hano Christophe, Bilal Haider Abbasi

Subject: Biology, Plant Sciences Keywords: Antioxidant; Anti-inflammatory; Chitosan; Flavonoids; Phenolics; Silybum marianum

Online: 11 January 2021 (15:59:31 CET)

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Silybum marianum (L.) Gaertn is a rich source of antioxidants and anti-inflammatory flavonolignans with great potential for use in pharmaceutical and cosmetic products. Its biotechnological production using in vitro culture system has been proposed. Chitosan is a well-known elicitor that strongly affects both secondary metabolites and biomass production by plants. The effect of chitosan on S. marianum cell suspension is not known yet. In the present study, suspension cultures of S marianum were exploited for their in vitro potency to produce bioactive flavonolignans in the presence of chitosan. Established cell suspension culture was maintained on the same hormonal media supplemented with 0.5 mg/L BAP (6-benzylaminopurine) and 1.0 mg/L NAA (α-naphthalene acetic acid) under photoperiod 16/8 h (light/dark) and exposed to various treatments of chitosan (ranging from 0.5 to 50.0 mg/L). The highest biomass production was observed for cell suspension treated with 5.0 mg/L chitosan, resulting in 123.3 g/L fresh weight (FW) and 17.7 g/L dry weight (DW) productions. Chitosan treatment resulted in an overall increase in the accumulation of flavonoids, phenolic compounds and silymarin. High accumulation levels of silybin B, silydianin and silybin A were recorded by HPLC analysis. The corresponding extracts displayed interesting antioxidant and anti-inflammatory capacities. In particular, high ABTS antioxidant activity (741.5 μM Trolox C equivalent antioxidant capacity) was recorded in extracts obtained in presence of 0.5 mg/L of chitosan. On the opposite, highest inhibitions of cyclooxygenase 2 (COX-2, 30.5 %), secretory phospholipase A2 (sPLA2, 33.9 %) and 15-lipoxygenase (15-LOX-2, 31.6 %) enzymes involved in inflammation process were measured in extracts obtained in presence of 5.0 mg/L of chitosan. Taken together, these results highlight the high potential of the chitosan elicitation of the S. marianum cell suspension for enhanced production of antioxidant and anti-inflammatory silymarin-rich extracts.

Preprint ARTICLE | doi:10.20944/preprints202101.0060.v1

A Computational Study for Identifying Agronomically Essential Biomarkers Using nsSNP Data of Korean Soybeans

Yongwoon Jung, Nahyun You, Sangyong Nam

Subject: Biology, Plant Sciences Keywords: Korean soybean varieties; nsSNP; Biomarker; SIFT; Polyphen; PANTHER; I-mutant 2.0

Online: 4 January 2021 (16:25:22 CET)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints202101.0034.v1

A ClearSee-Based Clearing Protocol for 3D Visualization of Arabidopsis thaliana Embryos

Ayame Imoto, Mitsuhiro Aida

Subject: Biology, Plant Sciences Keywords: clearing; 3D imaging; Arabidopsis thaliana; embryo; confocal microscopy; cell wall staining; fluorescent reporter; GFP

Online: 4 January 2021 (12:34:36 CET)

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Preprint HYPOTHESIS | doi:10.20944/preprints202010.0518.v1

Plant Sexual Reproduction: Perhaps the current plant two-sex model should be replaced with three- and four-sex models?

Scott Meissner

Subject: Biology, Plant Sciences Keywords: alternation of generations; fertilization; gametophyte; mating; meiosis; plant sexual reproduction; sporophyte

Online: 26 October 2020 (11:49:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202010.0255.v1

Characterization of Pathogen Air-Borne Inoculum Density by Information Theoretic Analysis of Spore Trap Time Series Data

Robin A Choudhury, Neil McRoberts

Subject: Biology, Plant Sciences Keywords: time series; entropy; average mutual information; stochastic process; deterministic dynamics

Online: 12 October 2020 (16:12:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0454.v1

Contribution of the Wild Food Plants in the Food System of Tribal Belt of Pakistan; The Pak - Afghan Border Region

Shujaul Mulk Khan, Abdullah Abdullah

Subject: Biology, Plant Sciences Keywords: gastronomy; livelihood; public healthcare; traditional knowledge; wild food plants; tribal belt

Online: 19 September 2020 (10:05:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0285.v1

Callus Culture of Ocimum basilicum L. cv 'Thai Basil' Is an Effective Biological System for the Production of Antioxidants Compared to Leaves

Saher Nazir, Hasnain Jan, Duangjai Tungmunnithum, Samantha Drouet, Muhammad Zia, Christophe Hano, Bilal Haider Abbasi

Subject: Biology, Plant Sciences Keywords: Antioxidants; Biological System; Caffeic Acid; Callus culture; Chicoric Acid; Phenolics; Plant in vitro Cultures; Rosmarinic Acid; Thai Basil

Online: 13 September 2020 (12:18:48 CEST)

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Thai basil is a renowned medicinal plant and a rich source of bioactive antioxidant compounds having several health benefits, with actions to prevent of cancer, diabetes and cardiovascular disease. Plant cell and tissue culture technologies can be routinely established as an important, sustainable and low-cost biomass source for the production of high-value phytochemicals. The current study aimed at developing an effective protocol for the production of Thai basil leaf derived callus cultures with sustainable and high production of biomass and antioxidants as an alternative of leaves production. MS basal medium with various concentrations of plant growth regulators (PGRs) compatible with nutraceutical applications (i.e., gibberellic acid (GA3) and 6-benzylaminopurine (BAP) either alone or in combination with naphthalene acetic acid (NAA)) were evaluated. Among all tested PGRs, the combination BAP:NAA (5 mg/L:1 mg/L) yield maximum biomass accumulation (fresh weight (FW): 190 g/L and dry weight (DW): 13.05 g/L) as well as enhanced phenolic (346.08 mg/L) production. HPLC quantification analysis indicated high productions of chicoric acid (35.77 mg/g DW) and rosmarinic acid (7.35 mg/g DW) under optimized callus culture conditions. Antioxidant potential was assessed using both in vitro cell free and in vivo cellular antioxidant assays. Maximum in vitro antioxidant activity DPPH (93.2 % of radical scavenging activity) and ABTS (1322 µM Trolox equivalent antioxidant capacity) was also observed for the extracts from callus cultures grown on optimal conditions. In vivo cellular antioxidant activity assay confirmed the effective protection against oxidative stress of the corresponding extract by the maximum inhibition of ROS and RNS production. Compared to commercial leaves, callus extracts showed higher production of chicoric acid and rosmarinic acid associated with higher antioxidant capacity. In addition, this biological system also has a large capacity for continuous biomass production, thus demonstrating its high potential for possible nutraceutical applications.

Preprint REVIEW | doi:10.20944/preprints202009.0276.v1

Biosynthesis of Lemongrass Essential Oil and the Underlying Mechanism for Its Insecticidal Activity

Mohammad Mukarram, M. Masroor A. Khan, Andleeb Zehra, Sadaf Choudhary, Tariq Aftab, M. Naeem

Subject: Biology, Plant Sciences Keywords: Citral; essential oil; integrated pest management; insect-repellent; lemongrass; MEP pathway; mevalonate pathway

Online: 13 September 2020 (11:30:41 CEST)

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Preprint REVIEW | doi:10.20944/preprints202009.0182.v1

Taxonomy and Phylogenetic Research on Ralstonia solanacearum: A Complex Pathogen with Extraordinary Economic Consequences

Sujan Paudel, Shefali Dobhal, Anne M. Alvarez, Mohammad Arif

Subject: Biology, Plant Sciences Keywords: Ralstonia solanacearum species complex; taxonomy; phylogenomic; plant bacteria; tomato wilt; bacterial wilt; brown rot of potato; Granville Wilt of tobacco; moko disease of banana; Bugtok disease; spewy eye

Online: 8 September 2020 (10:19:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0083.v1

Evidence of a Possible Double Hybrid Origin for Two Malagasy Species of Piper L. (Piperaceae)

Enrico Palchetti, Massimo Gori, Stefano Biricolti, Alessandro Calamai, Lorenzo Bini, Sara Falsini, Emilio Corti, Alessio Papini

Subject: Biology, Plant Sciences Keywords: Piper malgassicum; Piper tsarasotrae; Piperaceae; chromosomes; hybridization; DNA sequences; G3PDH; trnL; ndhF; Malagasy biodiversity

Online: 4 September 2020 (11:01:32 CEST)

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two new species of genus Piper L. from Madagascar: Piper malgassicum and Piper tsarasotrae, were analyzed to investigate their phylogenetic position and evolutionary history. Both plastidial and nuclear markers were used for sequencing. The plastidial markers (ndhF and the trnL intron) showed a close relationship between the two species with respect to the other species of Piper. Both species appeared phylogenetically related to the African P. guineense and the Malagasian/Mascarenhas endemic P. borbonense. The nuclear marker (G3PDH) amplification produced two separate sets of sequences: “long” sequences, that could be easily translated into an amino acid chain, and “short” sequences, characterized by deletions that did not allowed to translate them correctly to an amino acid sequence. Analyzing together the nuclear sequences, we observed that the “long” sequence of P. tsarasotrae had a stricter relationship to the African accessions of P. guineense, while the accession of P. malgassicum was more strictly related to P. borbonense. On the contrary both “short” sequences of Piper malgassicum and Piper tsaratsotrae resulted phylogenetically related to Asian accessions and more distantly related to the formerly cited species. This unexpected result was tentatively explained with a more ancient hybridization event between an ancestor of P. malgassicum and P. tsarasotrae (and possibly P. borbonense) and an Asian species of Piper. The Asian contribution would have produced the ancestors of the “short” sequences that would eventually have lost functionality by deletions, becoming paralogs. A more recent hybridization event would have led to the separation of Piper malgassicum from Piper tsarasotrae with an African pollen-derived genome contribution from P. guineense or, more probably, an ancestor thereof, to an ancestor of P. tsarasotrae. The chromosome numbers of P. tsarasotrae (2n = about 38) and P. malgassicum (2n = about 46), were more like the Asian species than to the American species. Unfortunately, no chromosome number of the African species P. guineense is currently available, to analyze eventual chromosomal connections.

Preprint ARTICLE | doi:10.20944/preprints202008.0702.v1

An Integrated Analytical Approach Reveals Trichome Acylsugar Metabolite Diversity in the Wild Tomato Solanum Pennellii

Daniel B. Lybrand, Thilani M. Anthony, Arthur Daniel Jones, Robert L. Last

Subject: Biology, Plant Sciences Keywords: acylsugar; wild tomato; Solanum pennellii; secretory glandular trichome; specialized metabolism; intraspecific variation; metabolomics

Online: 31 August 2020 (05:15:08 CEST)

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Preprint REVIEW | doi:10.20944/preprints202008.0642.v1

Gigantea: Uncovering New Functions in Flower Development

Claudio Brandoli, Cesar Petri, Marcos Egea-Cortines, Julia Weiss

Subject: Biology, Plant Sciences Keywords: gene ontology; molecular function; cellular localization; biological function; circadian clock; flowering time; flower development; floral scent

Online: 28 August 2020 (11:42:40 CEST)

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BIOLOGY