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Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications

BACKGROUND: The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional di...

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Autores principales: Yu, Jingyin, Tehrim, Sadia, Wang, Linhai, Dossa, Komivi, Zhang, Xiurong, Ke, Tao, Liao, Boshou
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604286/
https://www.ncbi.nlm.nih.gov/pubmed/28923019
http://dx.doi.org/10.1186/s12864-017-4094-7
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author Yu, Jingyin
Tehrim, Sadia
Wang, Linhai
Dossa, Komivi
Zhang, Xiurong
Ke, Tao
Liao, Boshou
author_facet Yu, Jingyin
Tehrim, Sadia
Wang, Linhai
Dossa, Komivi
Zhang, Xiurong
Ke, Tao
Liao, Boshou
author_sort Yu, Jingyin
collection PubMed
description BACKGROUND: The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. RESULTS: Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1.4-fold as many P450 members as A. thaliana. Most P450s in A. thaliana and Brassica species were located on pseudo-chromosomes. The inferred phylogeny indicated that all P450s were clustered into two different subgroups. Analysis of WGD event revealed that different P450 gene families had appeared after evolutionary events of species. For the TD event analyses, the P450s from TD events in Brassica species can be divided into ancient and recent parts. Our comparison of influence of WGD and TD events on the P450 gene superfamily between A. thaliana and Brassica species indicated that the family-specific evolution in the Brassica lineage can be attributed to both WGD and TD, whereas WGD was recognized as the major mechanism for the recent evolution of the P450 super gene family. Expression analysis of P450s from A. thaliana and Brassica species indicated that WGD-type P450s showed the same expression pattern but completely different expression with TD-type P450s across different tissues in Brassica species. Selection force analysis suggested that P450 orthologous gene pairs between A. thaliana and Brassica species underwent negative selection, but no significant differences were found between P450 orthologous gene pairs in A. thaliana–B. rapa and A. thaliana–B. oleracea lineages, as well as in different subgenomes in B. rapa or B. oleracea compared with A. thaliana. CONCLUSIONS: This study is the first to investigate the effects of WGD and TD on the evolutionary history and functional divergence of P450 gene families in A. thaliana and Brassica species. This study provides a biology model to study the mechanism of gene family formation, particularly in the context of the evolutionary history of angiosperms, and offers novel insights for the study of angiosperm genomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4094-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-56042862017-09-21 Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications Yu, Jingyin Tehrim, Sadia Wang, Linhai Dossa, Komivi Zhang, Xiurong Ke, Tao Liao, Boshou BMC Genomics Research Article BACKGROUND: The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. RESULTS: Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1.4-fold as many P450 members as A. thaliana. Most P450s in A. thaliana and Brassica species were located on pseudo-chromosomes. The inferred phylogeny indicated that all P450s were clustered into two different subgroups. Analysis of WGD event revealed that different P450 gene families had appeared after evolutionary events of species. For the TD event analyses, the P450s from TD events in Brassica species can be divided into ancient and recent parts. Our comparison of influence of WGD and TD events on the P450 gene superfamily between A. thaliana and Brassica species indicated that the family-specific evolution in the Brassica lineage can be attributed to both WGD and TD, whereas WGD was recognized as the major mechanism for the recent evolution of the P450 super gene family. Expression analysis of P450s from A. thaliana and Brassica species indicated that WGD-type P450s showed the same expression pattern but completely different expression with TD-type P450s across different tissues in Brassica species. Selection force analysis suggested that P450 orthologous gene pairs between A. thaliana and Brassica species underwent negative selection, but no significant differences were found between P450 orthologous gene pairs in A. thaliana–B. rapa and A. thaliana–B. oleracea lineages, as well as in different subgenomes in B. rapa or B. oleracea compared with A. thaliana. CONCLUSIONS: This study is the first to investigate the effects of WGD and TD on the evolutionary history and functional divergence of P450 gene families in A. thaliana and Brassica species. This study provides a biology model to study the mechanism of gene family formation, particularly in the context of the evolutionary history of angiosperms, and offers novel insights for the study of angiosperm genomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4094-7) contains supplementary material, which is available to authorized users. BioMed Central 2017-09-18 /pmc/articles/PMC5604286/ /pubmed/28923019 http://dx.doi.org/10.1186/s12864-017-4094-7 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.
spellingShingle Research Article
Yu, Jingyin
Tehrim, Sadia
Wang, Linhai
Dossa, Komivi
Zhang, Xiurong
Ke, Tao
Liao, Boshou
Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications
title Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications
title_full Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications
title_fullStr Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications
title_full_unstemmed Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications
title_short Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications
title_sort evolutionary history and functional divergence of the cytochrome p450 gene superfamily between arabidopsis thaliana and brassica species uncover effects of whole genome and tandem duplications
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604286/
https://www.ncbi.nlm.nih.gov/pubmed/28923019
http://dx.doi.org/10.1186/s12864-017-4094-7
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