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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.

Evolution history of duplicatedsmad3genes in teleost: insights from Japanese flounder,Paralichthys olivaceus