Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus

Following the two rounds of whole-genome duplication (WGD) during deuterosome evolution, a third genome duplication occurred in the ray-fined fish lineage and is considered to be responsible for the teleost-specific lineage diversification and regulation mechanisms. As a receptor-regulated SMAD (R-S...

Full description

Bibliographic Details
Main Authors:	Du, Xinxin, Liu, Yuezhong, Liu, Jinxiang, Zhang, Quanqi, Wang, Xubo
Format:	Online
Language:	English
Published:	PeerJ Inc. 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045880/

id	pubmed-5045880
recordtype	oai_dc
spelling	pubmed-50458802016-10-04 Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus Du, Xinxin Liu, Yuezhong Liu, Jinxiang Zhang, Quanqi Wang, Xubo Aquaculture, Fisheries and Fish Science Following the two rounds of whole-genome duplication (WGD) during deuterosome evolution, a third genome duplication occurred in the ray-fined fish lineage and is considered to be responsible for the teleost-specific lineage diversification and regulation mechanisms. As a receptor-regulated SMAD (R-SMAD), the function of SMAD3 was widely studied in mammals. However, limited information of its role or putative paralogs is available in ray-finned fishes. In this study, two SMAD3 paralogs were first identified in the transcriptome and genome of Japanese flounder (Paralichthys olivaceus). We also explored SMAD3 duplication in other selected species. Following identification, genomic structure, phylogenetic reconstruction, and synteny analyses performed by MrBayes and online bioinformatic tools confirmed that smad3a/3b most likely originated from the teleost-specific WGD. Additionally, selection pressure analysis and expression pattern of the two genes performed by PAML and quantitative real-time PCR (qRT-PCR) revealed evidence of subfunctionalization of the two SMAD3 paralogs in teleost. Our results indicate that two SMAD3 genes originate from teleost-specific WGD, remain transcriptionally active, and may have likely undergone subfunctionalization. This study provides novel insights to the evolution fates of smad3a/3b and draws attentions to future function analysis of SMAD3 gene family. PeerJ Inc. 2016-09-27 /pmc/articles/PMC5045880/ /pubmed/27703851 http://dx.doi.org/10.7717/peerj.2500 Text en © 2016 Du et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Du, Xinxin Liu, Yuezhong Liu, Jinxiang Zhang, Quanqi Wang, Xubo
spellingShingle	Du, Xinxin Liu, Yuezhong Liu, Jinxiang Zhang, Quanqi Wang, Xubo Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus
author_facet	Du, Xinxin Liu, Yuezhong Liu, Jinxiang Zhang, Quanqi Wang, Xubo
author_sort	Du, Xinxin
title	Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus
title_short	Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus
title_full	Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus
title_fullStr	Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus
title_full_unstemmed	Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus
title_sort	evolution history of duplicated smad3 genes in teleost: insights from japanese flounder, paralichthys olivaceus
description	Following the two rounds of whole-genome duplication (WGD) during deuterosome evolution, a third genome duplication occurred in the ray-fined fish lineage and is considered to be responsible for the teleost-specific lineage diversification and regulation mechanisms. As a receptor-regulated SMAD (R-SMAD), the function of SMAD3 was widely studied in mammals. However, limited information of its role or putative paralogs is available in ray-finned fishes. In this study, two SMAD3 paralogs were first identified in the transcriptome and genome of Japanese flounder (Paralichthys olivaceus). We also explored SMAD3 duplication in other selected species. Following identification, genomic structure, phylogenetic reconstruction, and synteny analyses performed by MrBayes and online bioinformatic tools confirmed that smad3a/3b most likely originated from the teleost-specific WGD. Additionally, selection pressure analysis and expression pattern of the two genes performed by PAML and quantitative real-time PCR (qRT-PCR) revealed evidence of subfunctionalization of the two SMAD3 paralogs in teleost. Our results indicate that two SMAD3 genes originate from teleost-specific WGD, remain transcriptionally active, and may have likely undergone subfunctionalization. This study provides novel insights to the evolution fates of smad3a/3b and draws attentions to future function analysis of SMAD3 gene family.
publisher	PeerJ Inc.
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045880/
_version_	1613669075661094912

Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus

Similar Items