AUTHOR=Huang Xu , Wu Chang , Gong Kaijun , Chen Qian , Gu Qianhong , Qin Huan , Zhao Chun , Yu Tingting , Yang Li , Fu Wen , Wang Yude , Qin Qinbo , Liu Shaojun 

TITLE=Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00804

DOI=10.3389/fgene.2020.00804

ISSN=1664-8021

ABSTRACT=<p>The <italic>Sox</italic> gene family encoded transcription factors that played key roles in developmental processes in vertebrates. To further understand the evolutionary fate of the <italic>Sox</italic> gene family in teleosts, the <italic>Sox</italic> genes were comprehensively characterized in fish of different ploidy levels, including blunt snout bream (2n = 48, <italic>Megalobrama amblycephala</italic>, BSB), goldfish (2n = 100, <italic>Carassius auratus</italic> red var., 2nRCC), and autotetraploid <italic>C. auratus</italic> (4n = 200, 4nRCC). The 4nRCC, which derived from the whole genome duplication (WGD) of 2nRCC, were obtained through the distant hybridization of 2nRCC (♀) × BSB (♂). Compared with the 26 <italic>Sox</italic> genes in zebrafish (2n = 50, <italic>Danio rerio</italic>), 26, 47, and 92 putative <italic>Sox</italic> genes were identified in the BSB, 2nRCC, and 4nRCC genomes, respectively, and classified into seven subfamilies (B1, B2, C, D, E, F, and K). Comparative analyses showed that 89.36% (42/47) of <italic>Sox</italic> genes were duplicated in 2nRCC compared with those in BSB, while 97.83% (90/92) of <italic>Sox</italic> genes were duplicated in 4nRCC compared with those in 2nRCC, meaning the <italic>Sox</italic> gene family had undergone an expansion in BSB, 2nRCC, and 4nRCC, respectively, following polyploidization events. In addition, potential gene loss, genetic variations, and paternal parent SNP locus insertion occurred during the polyploidization events. Our data provided new insights into the evolution of the <italic>Sox</italic> gene family in polyploid vertebrates after several rounds of WGD events.</p>