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Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean

BACKGROUND: Previous studies suggest that the metabolic pathway structure influences the selection and evolution rates of involved genes. However, most of these studies have exclusively considered a single gene copy encoding each enzyme in the metabolic pathway. Considering multiple-copy encoding en...

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Autores principales: Chu, Shanshan, Wang, Jiao, Cheng, Hao, Yang, Qing, Yu, Deyue
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076065/
https://www.ncbi.nlm.nih.gov/pubmed/24962214
http://dx.doi.org/10.1186/1471-2156-15-76
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author Chu, Shanshan
Wang, Jiao
Cheng, Hao
Yang, Qing
Yu, Deyue
author_facet Chu, Shanshan
Wang, Jiao
Cheng, Hao
Yang, Qing
Yu, Deyue
author_sort Chu, Shanshan
collection PubMed
description BACKGROUND: Previous studies suggest that the metabolic pathway structure influences the selection and evolution rates of involved genes. However, most of these studies have exclusively considered a single gene copy encoding each enzyme in the metabolic pathway. Considering multiple-copy encoding enzymes could provide direct evidence of gene evolution and duplication patterns in metabolic pathways. We conducted a detailed analysis of the phylogeny, synteny, evolutionary rate and selection pressure of the genes in the isoflavonoid metabolic pathway of soybeans. RESULTS: The results revealed that 1) only the phenylalanine ammonia-lyase (PAL) gene family most upstream from the pathway preserved all of the ancient and recent segmental duplications and maintained a strongly conserved synteny among these duplicated segments; gene families encoding branch-point enzymes with higher pleiotropy tended to retain more types of duplication; and genes encoding chalcone reductase (CHR) and isoflavone synthase (IFS) specific for legumes retained only recent segmental duplications; 2) downstream genes evolved faster than upstream genes and were subject to positive selection or relaxed selection constraints; 3) gene members encoding enzymes with high pleiotropy at the branching points were more likely to have undergone evolutionary differentiation, which may correspond to their functional divergences. CONCLUSIONS: We reconciled our results with existing controversies and proposed that gene copies at branch points with higher connectivity might be under stronger selective constraints and that the gene copies controlling metabolic flux allocation underwent positive selection. Our analyses demonstrated that the structure and function of a metabolic pathway shapes gene duplication and the evolutionary constraints of constituent enzymes.
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spelling pubmed-40760652014-07-01 Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean Chu, Shanshan Wang, Jiao Cheng, Hao Yang, Qing Yu, Deyue BMC Genet Research Article BACKGROUND: Previous studies suggest that the metabolic pathway structure influences the selection and evolution rates of involved genes. However, most of these studies have exclusively considered a single gene copy encoding each enzyme in the metabolic pathway. Considering multiple-copy encoding enzymes could provide direct evidence of gene evolution and duplication patterns in metabolic pathways. We conducted a detailed analysis of the phylogeny, synteny, evolutionary rate and selection pressure of the genes in the isoflavonoid metabolic pathway of soybeans. RESULTS: The results revealed that 1) only the phenylalanine ammonia-lyase (PAL) gene family most upstream from the pathway preserved all of the ancient and recent segmental duplications and maintained a strongly conserved synteny among these duplicated segments; gene families encoding branch-point enzymes with higher pleiotropy tended to retain more types of duplication; and genes encoding chalcone reductase (CHR) and isoflavone synthase (IFS) specific for legumes retained only recent segmental duplications; 2) downstream genes evolved faster than upstream genes and were subject to positive selection or relaxed selection constraints; 3) gene members encoding enzymes with high pleiotropy at the branching points were more likely to have undergone evolutionary differentiation, which may correspond to their functional divergences. CONCLUSIONS: We reconciled our results with existing controversies and proposed that gene copies at branch points with higher connectivity might be under stronger selective constraints and that the gene copies controlling metabolic flux allocation underwent positive selection. Our analyses demonstrated that the structure and function of a metabolic pathway shapes gene duplication and the evolutionary constraints of constituent enzymes. BioMed Central 2014-06-24 /pmc/articles/PMC4076065/ /pubmed/24962214 http://dx.doi.org/10.1186/1471-2156-15-76 Text en Copyright © 2014 Chu et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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
Chu, Shanshan
Wang, Jiao
Cheng, Hao
Yang, Qing
Yu, Deyue
Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean
title Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean
title_full Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean
title_fullStr Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean
title_full_unstemmed Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean
title_short Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean
title_sort evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076065/
https://www.ncbi.nlm.nih.gov/pubmed/24962214
http://dx.doi.org/10.1186/1471-2156-15-76
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