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Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants

BACKGROUND: Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Integrated phylogenomic synteny network analyses were able to provide novel insights into the evolution of the ARF gene family. RESULTS: Here, more than...

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Autores principales: Gao, Bei, Wang, Liuqiang, Oliver, Melvin, Chen, Moxian, Zhang, Jianhua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7226935/
https://www.ncbi.nlm.nih.gov/pubmed/32467718
http://dx.doi.org/10.1186/s13007-020-00609-1
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author Gao, Bei
Wang, Liuqiang
Oliver, Melvin
Chen, Moxian
Zhang, Jianhua
author_facet Gao, Bei
Wang, Liuqiang
Oliver, Melvin
Chen, Moxian
Zhang, Jianhua
author_sort Gao, Bei
collection PubMed
description BACKGROUND: Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Integrated phylogenomic synteny network analyses were able to provide novel insights into the evolution of the ARF gene family. RESULTS: Here, more than 3500 ARFs collected from plant genomes and transcriptomes covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting distinct groups. Recurrent duplication events, such as those that occurred in seed plants, angiosperms, core eudicots and grasses contributed to the expansion of ARF genes which facilitated functional diversification. Ancestral transposition activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may have accelerated the functional diversification process of paralogues. CONCLUSIONS: The broad-scale family phylogeny in combination with the state-of-art phylogenomic synteny network analyses not only allowed us to infer the evolutionary trajectory of ARF genes across distinct plant lineages, but also facilitated to generate a more robust classification regime for this transcription factor family. Our study provides insights into the evolution of ARFs which will enhance our current understanding of this important transcription factor family.
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spelling pubmed-72269352020-05-27 Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants Gao, Bei Wang, Liuqiang Oliver, Melvin Chen, Moxian Zhang, Jianhua Plant Methods Research BACKGROUND: Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Integrated phylogenomic synteny network analyses were able to provide novel insights into the evolution of the ARF gene family. RESULTS: Here, more than 3500 ARFs collected from plant genomes and transcriptomes covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting distinct groups. Recurrent duplication events, such as those that occurred in seed plants, angiosperms, core eudicots and grasses contributed to the expansion of ARF genes which facilitated functional diversification. Ancestral transposition activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may have accelerated the functional diversification process of paralogues. CONCLUSIONS: The broad-scale family phylogeny in combination with the state-of-art phylogenomic synteny network analyses not only allowed us to infer the evolutionary trajectory of ARF genes across distinct plant lineages, but also facilitated to generate a more robust classification regime for this transcription factor family. Our study provides insights into the evolution of ARFs which will enhance our current understanding of this important transcription factor family. BioMed Central 2020-05-14 /pmc/articles/PMC7226935/ /pubmed/32467718 http://dx.doi.org/10.1186/s13007-020-00609-1 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Gao, Bei
Wang, Liuqiang
Oliver, Melvin
Chen, Moxian
Zhang, Jianhua
Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
title Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
title_full Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
title_fullStr Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
title_full_unstemmed Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
title_short Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
title_sort phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7226935/
https://www.ncbi.nlm.nih.gov/pubmed/32467718
http://dx.doi.org/10.1186/s13007-020-00609-1
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