Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice

Abstract Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies,...

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Autores principales:	Muhammad-Redha Abdullah-Zawawi, Nur-Farhana Ahmad-Nizammuddin, Nisha Govender, Sarahani Harun, Norfarhan Mohd-Assaad, Zeti-Azura Mohamed-Hussein
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1eeda851b1fa455c87cc868d735e490f
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spelling	oai:doaj.org-article:1eeda851b1fa455c87cc868d735e490f2021-12-02T18:37:08ZComparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice10.1038/s41598-021-99206-y2045-2322https://doaj.org/article/1eeda851b1fa455c87cc868d735e490f2021-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-99206-yhttps://doaj.org/toc/2045-2322Abstract Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon–intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.Muhammad-Redha Abdullah-ZawawiNur-Farhana Ahmad-NizammuddinNisha GovenderSarahani HarunNorfarhan Mohd-AssaadZeti-Azura Mohamed-HusseinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-18 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Muhammad-Redha Abdullah-Zawawi Nur-Farhana Ahmad-Nizammuddin Nisha Govender Sarahani Harun Norfarhan Mohd-Assaad Zeti-Azura Mohamed-Hussein Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
description	Abstract Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon–intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.
format	article
author	Muhammad-Redha Abdullah-Zawawi Nur-Farhana Ahmad-Nizammuddin Nisha Govender Sarahani Harun Norfarhan Mohd-Assaad Zeti-Azura Mohamed-Hussein
author_facet	Muhammad-Redha Abdullah-Zawawi Nur-Farhana Ahmad-Nizammuddin Nisha Govender Sarahani Harun Norfarhan Mohd-Assaad Zeti-Azura Mohamed-Hussein
author_sort	Muhammad-Redha Abdullah-Zawawi
title	Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
title_short	Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
title_full	Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
title_fullStr	Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
title_full_unstemmed	Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
title_sort	comparative genome-wide analysis of wrky, mads-box and myb transcription factor families in arabidopsis and rice
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/1eeda851b1fa455c87cc868d735e490f
work_keys_str_mv	AT muhammadredhaabdullahzawawi comparativegenomewideanalysisofwrkymadsboxandmybtranscriptionfactorfamiliesinarabidopsisandrice AT nurfarhanaahmadnizammuddin comparativegenomewideanalysisofwrkymadsboxandmybtranscriptionfactorfamiliesinarabidopsisandrice AT nishagovender comparativegenomewideanalysisofwrkymadsboxandmybtranscriptionfactorfamiliesinarabidopsisandrice AT sarahaniharun comparativegenomewideanalysisofwrkymadsboxandmybtranscriptionfactorfamiliesinarabidopsisandrice AT norfarhanmohdassaad comparativegenomewideanalysisofwrkymadsboxandmybtranscriptionfactorfamiliesinarabidopsisandrice AT zetiazuramohamedhussein comparativegenomewideanalysisofwrkymadsboxandmybtranscriptionfactorfamiliesinarabidopsisandrice
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Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice

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