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Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata

Background: Kandelia obovata, a dominant mangrove species, is widely distributed in tropical and subtropical areas. Low temperature is the major abiotic stress that seriously limits the survival and growth of mangroves. WRKY transcription factors (TFs) play vital roles in responses to biotic and abi...

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Autores principales: Du, Zhaokui, You, Shixian, Zhao, Xin, Xiong, Lihu, Li, Junmin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9008847/
https://www.ncbi.nlm.nih.gov/pubmed/35432463
http://dx.doi.org/10.3389/fgene.2022.875316
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author Du, Zhaokui
You, Shixian
Zhao, Xin
Xiong, Lihu
Li, Junmin
author_facet Du, Zhaokui
You, Shixian
Zhao, Xin
Xiong, Lihu
Li, Junmin
author_sort Du, Zhaokui
collection PubMed
description Background: Kandelia obovata, a dominant mangrove species, is widely distributed in tropical and subtropical areas. Low temperature is the major abiotic stress that seriously limits the survival and growth of mangroves. WRKY transcription factors (TFs) play vital roles in responses to biotic and abiotic stresses. However, genome-wide analysis of WRKY genes in K. obovata and their responses to chilling stress have not been reported. Methods: Bioinformatic analysis was used to identify and characterize the K. obovata WRKY (KoWRKY) gene family, RNA-seq and qRT–PCR analyses were employed to screen KoWRKYs that respond to chilling stress. Results: Sixty-four KoWRKYs were identified and they were unevenly distributed across all 18 K. obovata chromosomes. Many orthologous WRKY gene pairs were identified between Arabidopsis thaliana and K. obovata, showing high synteny between the two genomes. Segmental duplication events were found to be the major force driving the expansion for the KoWRKY gene family. Most of the KoWRKY genes contained several kinds of hormone- and stress-responsive cis-elements in their promoter. KoWRKY proteins belonged to three groups (I, II, III) according to their conserved WRKY domains and zinc-finger structure. Expression patterns derived from the RNA-seq and qRT–PCR analyses revealed that 9 KoWRKYs were significantly upregulated during chilling acclimation in the leaves. KEGG pathway enrichment analysis showed that the target genes of KoWRKYs were significantly involved in 11 pathways, and coexpression network analysis showed that 315 coexpressed pairs (KoWRKYs and mRNAs) were positively correlated. Conclusion: Sixty-four KoWRKYs from the K. obovata genome were identified, 9 of which exhibited chilling stress-induced expression patterns. These genes represent candidates for future functional analysis of KoWRKYs involved in chilling stress related signaling pathways in K. obovata. Our results provide a basis for further analysis of KoWRKY genes to determine their functions and molecular mechanisms in K. obovata in response to chilling stress.
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spelling pubmed-90088472022-04-15 Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata Du, Zhaokui You, Shixian Zhao, Xin Xiong, Lihu Li, Junmin Front Genet Genetics Background: Kandelia obovata, a dominant mangrove species, is widely distributed in tropical and subtropical areas. Low temperature is the major abiotic stress that seriously limits the survival and growth of mangroves. WRKY transcription factors (TFs) play vital roles in responses to biotic and abiotic stresses. However, genome-wide analysis of WRKY genes in K. obovata and their responses to chilling stress have not been reported. Methods: Bioinformatic analysis was used to identify and characterize the K. obovata WRKY (KoWRKY) gene family, RNA-seq and qRT–PCR analyses were employed to screen KoWRKYs that respond to chilling stress. Results: Sixty-four KoWRKYs were identified and they were unevenly distributed across all 18 K. obovata chromosomes. Many orthologous WRKY gene pairs were identified between Arabidopsis thaliana and K. obovata, showing high synteny between the two genomes. Segmental duplication events were found to be the major force driving the expansion for the KoWRKY gene family. Most of the KoWRKY genes contained several kinds of hormone- and stress-responsive cis-elements in their promoter. KoWRKY proteins belonged to three groups (I, II, III) according to their conserved WRKY domains and zinc-finger structure. Expression patterns derived from the RNA-seq and qRT–PCR analyses revealed that 9 KoWRKYs were significantly upregulated during chilling acclimation in the leaves. KEGG pathway enrichment analysis showed that the target genes of KoWRKYs were significantly involved in 11 pathways, and coexpression network analysis showed that 315 coexpressed pairs (KoWRKYs and mRNAs) were positively correlated. Conclusion: Sixty-four KoWRKYs from the K. obovata genome were identified, 9 of which exhibited chilling stress-induced expression patterns. These genes represent candidates for future functional analysis of KoWRKYs involved in chilling stress related signaling pathways in K. obovata. Our results provide a basis for further analysis of KoWRKY genes to determine their functions and molecular mechanisms in K. obovata in response to chilling stress. Frontiers Media S.A. 2022-03-31 /pmc/articles/PMC9008847/ /pubmed/35432463 http://dx.doi.org/10.3389/fgene.2022.875316 Text en Copyright © 2022 Du, You, Zhao, Xiong and Li. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Du, Zhaokui
You, Shixian
Zhao, Xin
Xiong, Lihu
Li, Junmin
Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata
title Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata
title_full Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata
title_fullStr Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata
title_full_unstemmed Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata
title_short Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata
title_sort genome-wide identification of wrky genes and their responses to chilling stress in kandelia obovata
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9008847/
https://www.ncbi.nlm.nih.gov/pubmed/35432463
http://dx.doi.org/10.3389/fgene.2022.875316
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