Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction

Although the regulatory function of miRNAs and their targets have been characterized in model plants, a possible underlying role in the cotton response to herbivore infestation has not been determined. To investigate this, we performed small RNA and degradome sequencing between resistant and susceptible cotton cultivar following infestation with the generalist herbivore whitefly. In total, the 260 miRNA families and 241 targets were identified. Quantitative-PCR analysis revealed that several miRNAs and their corresponding targets exhibited dynamic spatio-temporal expression patterns. Moreover, 17 miRNA precursors were generated from 29 long intergenic non-coding RNA (lincRNA) transcripts. The genome-wide analysis also led to the identification of 85 phased small interfering RNA (phasiRNA) loci. Among these, nine PHAS genes were triggered by miR167, miR390, miR482a, and two novel miRNAs, including those encoding a leucine-rich repeat (LRR) disease resistance protein, an auxin response factor (ARF) and MYB transcription factors. Through combined modeling and experimental data, we explored and expanded the miR390-tasiARF cascade during the cotton response to whitefly. Virus-induced gene silencing (VIGS) of ARF8 from miR390 target in whitefly-resistant cotton plants increased auxin and jasmonic acid (JA) accumulation, resulting in increased tolerance to whitefly infestation. These results highlight the provides a useful transcriptomic resource for plant-herbivore interaction.

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Genome-Wide Analysis of Cotton miRNAs during Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction

10.20944/preprints201908.0287.v1 ◽

2019 ◽

Author(s):

Jianying Li ◽

J. Joe Hull ◽

Sijia Liang ◽

Qiongqiong Wang ◽

Luo Chen ◽

...

Keyword(s):

Expression Patterns ◽

Regulatory Function ◽

Pcr Analysis ◽

Virus Induced Gene Silencing ◽

Generalist Herbivore ◽

Genome Wide Analysis ◽

Genome Wide ◽

Plant Herbivore Interaction ◽

Plant Herbivore ◽

Herbivore Interaction

Although the regulatory function of miRNAs and their targets have been characterized in model plants, a possible underlying role in the cotton response to herbivore infestation has not been determined. To investigate this, we performed small RNA and degradome sequencing between resistant and susceptible cotton cultivar following infestation with the generalist herbivore whitefly. In total, 260 miRNA families and 241 targets were identified. Quantitative-PCR analysis revealed that several miRNAs and their corresponding targets exhibited dynamic spatio-temporal expression patterns. Moreover, 17 miRNA precursors were generated from 29 long intergenic non-coding RNA (lincRNA) transcripts. Genome-wide analysis also led to the identification of 85 phased small interfering RNA (phasiRNA) loci. Among these, nine PHAS genes were triggered by miR167, miR390, miR482a, and two novel miRNAs, including those encoding a leucine-rich repeat (LRR) disease resistance protein, an auxin response factor (ARF) and MYB transcription factors. Through combined modeling and experimental data, we explored and expanded the miR390-tasiARF cascade during the cotton response to whitefly. Virus-induced gene silencing (VIGS) of ARF8 in whitefly-resistant cotton plants increased auxin and jasmonic acid (JA) accumulation, resulting in an increased tolerance to whitefly infestation. These results highlight the provides a useful transcriptomic resource for plant-herbivore interaction.

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Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms19092478 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2478 ◽

Cited By ~ 15

Author(s):

Qinglong Dong ◽

Dingyue Duan ◽

Shuang Zhao ◽

Bingyao Xu ◽

Jiawei Luo ◽

...

Keyword(s):

Drought Tolerance ◽

Gene Family ◽

Transgenic Arabidopsis ◽

Abiotic Stress Tolerance ◽

Expression Patterns ◽

Pcr Analysis ◽

Sequence Alignments ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

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Faculty Opinions recommendation of Contrasting dynamics in the same plant-herbivore interaction.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1002022.201006 ◽

2003 ◽

Author(s):

Thomas Mitchell-Olds

Keyword(s):

Plant Herbivore Interaction ◽

Plant Herbivore ◽

Herbivore Interaction

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Roles of the 14-3-3 gene family in cotton flowering

BMC Plant Biology ◽

10.1186/s12870-021-02923-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Na Sang ◽

Hui Liu ◽

Bin Ma ◽

Xianzhong Huang ◽

Lu Zhuo ◽

...

Keyword(s):

Gene Family ◽

Protein Interactions ◽

Leucine Zipper ◽

Expression Patterns ◽

Bimolecular Fluorescence Complementation ◽

Structural Motif ◽

Virus Induced Gene Silencing ◽

Protein Protein Interactions ◽

Basic Leucine Zipper ◽

Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

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Evolutionary responses to environmental change: trophic interactions affect adaptation and persistence

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.1351 ◽

2015 ◽

Vol 282 (1805) ◽

pp. 20141351 ◽

Cited By ~ 14

Author(s):

Jarad P. Mellard ◽

Claire de Mazancourt ◽

Michel Loreau

Keyword(s):

Climate Change ◽

Head Start ◽

Trophic Interactions ◽

Evolutionary Dynamics ◽

Plant Interaction ◽

Persistence Time ◽

Plant Persistence ◽

Plant Herbivore Interaction ◽

Plant Herbivore ◽

Herbivore Interaction

According to recent reviews, the question of how trophic interactions may affect evolutionary responses to climate change remains unanswered. In this modelling study, we explore the evolutionary dynamics of thermal and plant–herbivore interaction traits in a warming environment. We find the herbivore usually reduces adaptation speed and persistence time of the plant by reducing biomass. However, if the plant interaction trait and thermal trait are correlated, herbivores can create different coevolutionary attractors. One attractor has a warmer plant thermal optimum, and the other a colder one compared with the environment. A warmer plant thermal strategy is given a head start under warming, the only case where herbivores can increase plant persistence under warming. Persistence time of the plant under warming is maximal at small or large thermal niche width. This study shows that considering trophic interactions is necessary and feasible for understanding how ecosystems respond to climate change.

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Geographic variation and temporal changes in plant–herbivore interaction: Case studies with Solidago altissima in native and introduced ranges

Plant Species Biology ◽

10.1111/1442-1984.12353 ◽

2021 ◽

Author(s):

Yuzu Sakata

Keyword(s):

Case Studies ◽

Geographic Variation ◽

Temporal Changes ◽

Solidago Altissima ◽

Plant Herbivore Interaction ◽

Native And Introduced Ranges ◽

Plant Herbivore ◽

Herbivore Interaction

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Genome-Wide Identification and Expression Profiling Analysis of the Galactinol Synthase Gene Family in Cassava (Manihot esculenta Crantz)

Agronomy ◽

10.3390/agronomy8110250 ◽

2018 ◽

Vol 8 (11) ◽

pp. 250 ◽

Cited By ~ 4

Author(s):

Ruimei Li ◽

Shuai Yuan ◽

Yingdui He ◽

Jie Fan ◽

Yangjiao Zhou ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Manihot Esculenta ◽

Expression Patterns ◽

Pcr Analysis ◽

Systematic Research ◽

Raffinose Family Oligosaccharides ◽

Manihot Esculenta Crantz ◽

Galactinol Synthase ◽

Genome Wide

Galactinol synthases (GolSs) are the key enzymes that participate in raffinose family oligosaccharides (RFO) biosynthesis, which perform a big role in modulating plant growth and response to biotic or abiotic stresses. To date, no systematic study of this gene family has been conducted in cassava (Manihot esculenta Crantz). Here, eight MeGolS genes are isolated from the cassava genome. Based on phylogenetic background, the MeGolSs are clustered into four groups. Through predicting the cis-elements in their promoters, it was discovered that all MeGolS members act as hormone-, stress-, and tissue-specific related elements to different degrees. MeGolS genes exhibit incongruous expression patterns in various tissues, indicating that different MeGolS proteins might have diverse functions. MeGolS1 and MeGolS3–6 are highly expressed in leaves and midveins. MeGolS3–6 are highly expressed in fibrous roots. Quantitative real-time Polymerase Chain Reaction (qRT-PCR) analysis indicates that several MeGolSs, including MeGolS1, 2, 5, 6, and 7, are induced by abiotic stresses. microRNA prediction analysis indicates that several abiotic stress-related miRNAs target the MeGolS genes, such as mes-miR156, 159, and 169, which also respond to abiotic stresses. The current study is the first systematic research of GolS genes in cassava, and the results of this study provide a basis for further exploration the functional mechanism of GolS genes in cassava.

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Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

10.21203/rs.2.22104/v1 ◽

2020 ◽

Author(s):

Yuxin Pan ◽

Jinpeng Wang ◽

Zhenyi Wang ◽

Hengwei Liu ◽

Lan Zhang ◽

...

Keyword(s):

Positive Selection ◽

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Subcellular Location ◽

Pcr Analysis ◽

Genome Wide ◽

Cotton Species ◽

Expressional Analysis ◽

Significant Positive Selection

Abstract Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

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