Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus.
Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus.
复制标题
硬骨鱼中重复 smad3 基因的进化历史：来自日本牙鲆、牙鲆的见解。
作者：
Du X;Liu Y;Liu J;Zhang Q;Wang X
在后体进化的两轮全基因组复制(WGD)之后，第三轮基因组复制发生在射线细长的鱼类谱系中，被认为是导致硬骨鱼特有的谱系多样化和调节机制的原因。作为一种受体调节的SMAD(R-SMAD)，Smad3的功能在哺乳动物中得到了广泛的研究。然而，关于它的作用或推定的副鱼的信息在鳍鱼中是有限的。在本研究中，首次在牙鲆(Paralichthys Olivaceus)的转录组和基因组中发现了两个Smad3同源基因。我们还探索了SMAD3在其他选定物种中的复制情况。经过鉴定、基因组结构、系统发育重建和同源性分析，贝叶斯先生和在线生物信息学工具证实，smad3a/3b很可能来自硬骨鱼特有的WGD。此外，PAML和实时定量聚合酶链式反应(qRT-PCR)对这两个基因进行了选择压力分析和表达谱分析，证实了这两个Smad3基因在硬骨鱼中的亚功能化。我们的结果表明，两个SMAD3基因起源于硬骨鱼特异性的WGD，保持转录活性，并可能经历了亚功能化。本研究为SMAD3a/3b基因的进化命运提供了新的见解，并为未来Smad3基因家族的功能分析提供了新的思路。
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.
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影响因子：
16.6
作者：
Berthelot, Camille;Brunet, Frederic;Chalopin, Domitille;Juanchich, Amelie;Bernard, Maria;Noel, Benjamin;Bento, Pascal;Da Silva, Corinne;Labadie, Karine;Alberti, Adriana;Aury, Jean-Marc;Louis, Alexandra;Dehais, Patrice;Bardou, Philippe;Montfort, Jerome;Klopp, Christophe;Cabau, Cedric;Gaspin, Christine;Thorgaard, Gary H.;Boussaha, Mekki;Quillet, Edwige;Guyomard, Rene;Galiana, Delphine;Bobe, Julien;Volff, Jean-Nicolas;Genet, Carine;Wincker, Patrick;Jaillon, Olivier;Roest Crollius, Hugues;Guiguen, Yann
通讯作者：
Guiguen, Yann
影响因子：
64.8
作者：
Aury, Jean-Marc;Jaillon, Olivier;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
7
作者：
Carmel, Liran;Rogozin, Igor B.;Koonin, Eugene V.
通讯作者：
Koonin, Eugene V.
影响因子：
11.4
作者：
Hoegg, S;Meyer, A
通讯作者：
Meyer, A
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS