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Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication

The genus Brassica contains a diverse group of important vegetables and oilseed crops. Genome sequencing has been completed for the six species (B. rapa, B. oleracea, B. nigra, B. carinata, B. napus, and B. juncea) in U’s triangle model. The purpose of the study is to investigate whether positively...

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Autores principales: Wei, Dayong, Li, Nan, Zhang, Nan, Liu, Feng, Wu, Jie, Zhao, Sa, Shen, Jinjuan, Wang, Zhimin, Peng, Lisha, Fan, Yonghong, Mei, Jiaqin, Tang, Qinglin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10110867/
https://www.ncbi.nlm.nih.gov/pubmed/37082337
http://dx.doi.org/10.3389/fpls.2023.1142147
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author Wei, Dayong
Li, Nan
Zhang, Nan
Liu, Feng
Wu, Jie
Zhao, Sa
Shen, Jinjuan
Wang, Zhimin
Peng, Lisha
Fan, Yonghong
Mei, Jiaqin
Tang, Qinglin
author_facet Wei, Dayong
Li, Nan
Zhang, Nan
Liu, Feng
Wu, Jie
Zhao, Sa
Shen, Jinjuan
Wang, Zhimin
Peng, Lisha
Fan, Yonghong
Mei, Jiaqin
Tang, Qinglin
author_sort Wei, Dayong
collection PubMed
description The genus Brassica contains a diverse group of important vegetables and oilseed crops. Genome sequencing has been completed for the six species (B. rapa, B. oleracea, B. nigra, B. carinata, B. napus, and B. juncea) in U’s triangle model. The purpose of the study is to investigate whether positively and negatively selected genes (PSGs and NSGs) affect gene feature and function differentiation of Brassica tetraploids in their evolution and domestication. A total of 9,701 PSGs were found in the A, B and C subgenomes of the three tetraploids, of which, a higher number of PSGs were identified in the C subgenome as comparing to the A and B subgenomes. The PSGs of the three tetraploids had more tandem duplicated genes, higher single copy, lower multi-copy, shorter exon length and fewer exon number than the NSGs, suggesting that the selective modes affected the gene feature of Brassica tetraploids. The PSGs of all the three tetraploids enriched in a few common KEGG pathways relating to environmental adaption (such as Phenylpropanoid biosynthesis, Riboflavin metabolism, Isoflavonoid biosynthesis, Plant-pathogen interaction and Tropane, piperidine and pyridine alkaloid biosynthesis) and reproduction (Homologous recombination). Whereas, the NSGs of the three tetraploids significantly enriched in dozens of biologic processes and pathways without clear relationships with evolution. Moreover, the PSGs of B. carinata were found specifically enriched in lipid biosynthesis and metabolism which possibly contributed to the domestication of B. carinata as an oil crop. Our data suggest that selective modes affected the gene feature of Brassica tetraploids, and PSGs contributed in not only the evolution but also the domestication of Brassica tetraploids.
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spelling pubmed-101108672023-04-19 Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication Wei, Dayong Li, Nan Zhang, Nan Liu, Feng Wu, Jie Zhao, Sa Shen, Jinjuan Wang, Zhimin Peng, Lisha Fan, Yonghong Mei, Jiaqin Tang, Qinglin Front Plant Sci Plant Science The genus Brassica contains a diverse group of important vegetables and oilseed crops. Genome sequencing has been completed for the six species (B. rapa, B. oleracea, B. nigra, B. carinata, B. napus, and B. juncea) in U’s triangle model. The purpose of the study is to investigate whether positively and negatively selected genes (PSGs and NSGs) affect gene feature and function differentiation of Brassica tetraploids in their evolution and domestication. A total of 9,701 PSGs were found in the A, B and C subgenomes of the three tetraploids, of which, a higher number of PSGs were identified in the C subgenome as comparing to the A and B subgenomes. The PSGs of the three tetraploids had more tandem duplicated genes, higher single copy, lower multi-copy, shorter exon length and fewer exon number than the NSGs, suggesting that the selective modes affected the gene feature of Brassica tetraploids. The PSGs of all the three tetraploids enriched in a few common KEGG pathways relating to environmental adaption (such as Phenylpropanoid biosynthesis, Riboflavin metabolism, Isoflavonoid biosynthesis, Plant-pathogen interaction and Tropane, piperidine and pyridine alkaloid biosynthesis) and reproduction (Homologous recombination). Whereas, the NSGs of the three tetraploids significantly enriched in dozens of biologic processes and pathways without clear relationships with evolution. Moreover, the PSGs of B. carinata were found specifically enriched in lipid biosynthesis and metabolism which possibly contributed to the domestication of B. carinata as an oil crop. Our data suggest that selective modes affected the gene feature of Brassica tetraploids, and PSGs contributed in not only the evolution but also the domestication of Brassica tetraploids. Frontiers Media S.A. 2023-04-04 /pmc/articles/PMC10110867/ /pubmed/37082337 http://dx.doi.org/10.3389/fpls.2023.1142147 Text en Copyright © 2023 Wei, Li, Zhang, Liu, Wu, Zhao, Shen, Wang, Peng, Fan, Mei and Tang 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 Plant Science
Wei, Dayong
Li, Nan
Zhang, Nan
Liu, Feng
Wu, Jie
Zhao, Sa
Shen, Jinjuan
Wang, Zhimin
Peng, Lisha
Fan, Yonghong
Mei, Jiaqin
Tang, Qinglin
Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication
title Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication
title_full Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication
title_fullStr Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication
title_full_unstemmed Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication
title_short Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication
title_sort selective modes affect gene feature and function differentiation of tetraploid brassica species in their evolution and domestication
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10110867/
https://www.ncbi.nlm.nih.gov/pubmed/37082337
http://dx.doi.org/10.3389/fpls.2023.1142147
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