Meta-Analysis of Common and Differential Transcriptomic Responses to Biotic and Abiotic Stresses in Arabidopsis thaliana

Biniaz, Yaser; Tahmasebi, Aminallah; Afsharifar, Alireza; Tahmasebi, Ahmad; Poczai, Péter

doi:10.3390/plants11040502

Cited by 12 publications

(8 citation statements)

References 106 publications

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“…Field-grown plants experience numerous biotic stresses and respond by changing their transcriptome in a coordinated way. Although these changes depend on the particular stress encountered, prior research has shown that all stresses have a similar core response 27 , 29 . By comparing similarities between related, independent studies, it is possible to find the common genes most strongly linked to the trait under investigation and shortlist them for functional analysis 37 .…”

Section: Discussionmentioning

confidence: 99%

“…Though varied in number, MYB, ERF, bHLH, C2H2-ZF, C2C2, WRKY, and NAC family games were most dynamic in response to the studied seven diseases. The WRKY and NAC families are the source of most transcription factors (TFs) involved in pathogen defense mechanisms and responses 27 , 54 , 55 . These gene families contribute to plant immunity by differentially regulating defense-related gene expression.…”

Section: Discussionmentioning

confidence: 99%

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Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Hazra,

Ghosh,

Naskar

et al. 2023

Sci Rep

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Fungal infections are the inevitable limiting factor for productivity of tea. Transcriptome reprogramming recruits multiple regulatory pathways during pathogen infection. A comprehensive meta-analysis was performed utilizing previously reported, well-replicated transcriptomic datasets from seven fungal diseases of tea. The study identified a cumulative set of 18,517 differentially expressed genes (DEGs) in tea, implicated in several functional clusters, including the MAPK signaling pathway, transcriptional regulation, and the biosynthesis of phenylpropanoids. Gene set enrichment analyses under each pathogen stress elucidated that DEGs were involved in ethylene metabolism, secondary metabolism, receptor kinase activity, and various reactive oxygen species detoxification enzyme activities. Expressional fold change of combined datasets highlighting 2258 meta-DEGs shared a common transcriptomic response upon fungal stress in tea. Pervasive duplication events caused biotic stress-responsive core DEGs to appear in multiple copies throughout the tea genome. The co-expression network of meta-DEGs in multiple modules demonstrated the coordination of appropriate pathways, most of which involved cell wall organization. The functional coordination was controlled by a number of hub genes and miRNAs, leading to pathogenic resistance or susceptibility. This first-of-its-kind meta-analysis of host–pathogen interaction generated consensus candidate loci as molecular signatures, which can be associated with future resistance breeding programs in tea.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Hazra,

Ghosh,

Naskar

et al. 2023

Sci Rep

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show abstract

“…In the model plants, microRNA159 ( Ath - miR159 a,b,c) is a highly preserved miRNA in plants and contributes to stress responses [ 63 ]. Ath- miR5658 , Ath - miR858 , and Ath - miR1886 were also found to be responses to various stress tolerances [ 64 , 65 , 66 ]. In this work, we identified several miRNAs from Arabidopsis and P. patens that theoretically target overrepresented TF families in S. caninervis , similar to previous report s , stress-related miRNAs also target many TFs in S. caninervis , such as Ath-miR5658 potentially targeted four ScTF s members (Sc_ g03411_bHLH , Sc_g06422_ERF , and Sc_g02274_MYB ) and Ath-miR159 can specifically target Sc _ g13935_MYB.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization and Expression Analysis of Transcription Factor Families in Desert Moss Syntrichia caninervis under Abiotic Stresses

Salih

Bai

Zhao

et al. 2023

IJMS

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Transcription factor (TF) families play important roles in plant stress responses. S. caninervis is a new model moss for plant desiccation tolerance studies. Here, we report a high-confidence identification and characterization of 591 TFs representing 52 families that covered all chromosomes in S. caninervis. GO term and KEGG pathway analysis showed that TFs were involved in the regulation of transcription, DNA-templated, gene expression, binding activities, plant hormone signal transduction, and circadian rhythm. A number of TF promoter regions have a mixture of various hormones-related cis-regulatory elements. AP2/ERF, bHLH, MYB, and C2H2-zinc finger TFs were the overrepresented TF families in S. caninervis, and the detailed classification of each family is performed based on structural features. Transcriptome analysis revealed the transcript abundances of some ScAP2/ERF, bHLH, MYB, and C2H2 genes were accumulated in the treated S. caninervis under cold, dehydration, and rehydration stresses. The RT-qPCR results strongly agreed with RNA-seq analysis, indicating these TFs might play a key role in S. caninervis response to abiotic stress. Our comparative TF characterization and classification provide the foundations for functional investigations of the dominant TF genes involved in S. caninervis stress response, as well as excellent stress tolerance gene resources for plant stress resistance breeding.

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“…Among the lncRNA interactions with positive values is MIR5658, a long noncoding NAT detected here upregulated in GSNO-treated and WS-2 seedlings, and downregulated in IAA-treated seedlings ( Supplementary Table S3 ). MIR5658 has already been identified in different plant species as involved in plant development, hormone signaling, and tolerance to abiotic stress ( Biniaz et al, 2022 ). This miRNA precursor directly upregulates the expression of AT3G25290, a member of auxin-responsive gene family, by targeting its promoter.…”

Section: Discussionmentioning

confidence: 99%

Noncoding RNAs responsive to nitric oxide and their protein-coding gene targets shed light on root hair formation in Arabidopsis thaliana

et al. 2022

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An overview of the total Arabidopsis thaliana transcriptome, described previously by our research group, pointed some noncoding RNA (ncRNA) as participants in the restoration of hair-root phenotype in A. thaliana rhd6 mutants, leading us to a deeper investigation. A transcriptional gene expression profiling of seedling roots was performed aiming to identify ncRNA responsive to nitric oxide (GSNO) and auxin (IAA), and their involvement in root hair formation in the rhd6 null mutant. We identified 3,631 ncRNAs, including new ones, in A. thaliana and differential expression (DE) analysis between the following: 1) GSNO-treated rhd6 vs. untreated rhd6, 2) IAA-treated rhd6 vs. untreated rhd6, 3) GSNO-treated rhd6 vs. IAA-treated rhd6, and 4) WS-2 vs. untreated rhd6 detected the greatest number of DE genes in GSNO-treated rhd6. We detected hundreds of in silico interactions among ncRNA and protein-coding genes (PCGs), highlighting MIR5658 and MIR171 precursors highly upregulated in GSNO-treated rhd6 and wild type, respectively. Those ncRNA interact with many DE PCGs involved in hormone signaling, cell wall development, transcription factors, and root hair formation, becoming candidate genes in cell wall modulation and restoration of root hair phenotype by GSNO treatment. Our data shed light on how GSNO modulates ncRNA and their PCG targets in A. thaliana root hair formation.

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Meta-Analysis of Common and Differential Transcriptomic Responses to Biotic and Abiotic Stresses in Arabidopsis thaliana

Cited by 12 publications

References 106 publications

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Genome-Wide Characterization and Expression Analysis of Transcription Factor Families in Desert Moss Syntrichia caninervis under Abiotic Stresses

Noncoding RNAs responsive to nitric oxide and their protein-coding gene targets shed light on root hair formation in Arabidopsis thaliana

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