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
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Publicado: Nature Portfolio 2021
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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
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