Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice

Abstract WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza,...

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Autores principales:	Anne J. Villacastin, Keeley S. Adams, Rin Boonjue, Paul J. Rushton, Mira Han, Jeffery Q. Shen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/163b872a64a94f2485542a41013070b1
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spelling	oai:doaj.org-article:163b872a64a94f2485542a41013070b12021-12-02T16:50:23ZDynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice10.1038/s41598-021-94109-42045-2322https://doaj.org/article/163b872a64a94f2485542a41013070b12021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94109-4https://doaj.org/toc/2045-2322Abstract WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world’s most valued food crop.Anne J. VillacastinKeeley S. AdamsRin BoonjuePaul J. RushtonMira HanJeffery Q. ShenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anne J. Villacastin Keeley S. Adams Rin Boonjue Paul J. Rushton Mira Han Jeffery Q. Shen Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice
description	Abstract WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world’s most valued food crop.
format	article
author	Anne J. Villacastin Keeley S. Adams Rin Boonjue Paul J. Rushton Mira Han Jeffery Q. Shen
author_facet	Anne J. Villacastin Keeley S. Adams Rin Boonjue Paul J. Rushton Mira Han Jeffery Q. Shen
author_sort	Anne J. Villacastin
title	Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice
title_short	Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice
title_full	Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice
title_fullStr	Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice
title_full_unstemmed	Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice
title_sort	dynamic differential evolution schemes of wrky transcription factors in domesticated and wild rice
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/163b872a64a94f2485542a41013070b1
work_keys_str_mv	AT annejvillacastin dynamicdifferentialevolutionschemesofwrkytranscriptionfactorsindomesticatedandwildrice AT keeleysadams dynamicdifferentialevolutionschemesofwrkytranscriptionfactorsindomesticatedandwildrice AT rinboonjue dynamicdifferentialevolutionschemesofwrkytranscriptionfactorsindomesticatedandwildrice AT pauljrushton dynamicdifferentialevolutionschemesofwrkytranscriptionfactorsindomesticatedandwildrice AT mirahan dynamicdifferentialevolutionschemesofwrkytranscriptionfactorsindomesticatedandwildrice AT jefferyqshen dynamicdifferentialevolutionschemesofwrkytranscriptionfactorsindomesticatedandwildrice
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Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice

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