AUTHOR=Tuo Yun , Chu Wuying , Zhang Jianshe , Cheng Jia , Chen Lin , Bao Lingsheng , Xiao Tiaoyi 

TITLE=Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00714

DOI=10.3389/fgene.2020.00714

ISSN=1664-8021

ABSTRACT=<p><italic>Spinibarbus caldwelli</italic> is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of <italic>S. caldwelli</italic>, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by <italic>de novo</italic> assembly. Additionally, we calculated that the divergence time between <italic>S. caldwelli</italic> and <italic>Sinocyclocheilus grahami</italic> is 23.14 million years ago (Mya). And both of them diverged from <italic>Ctenopharyngodon idellus</italic> 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as <italic>POLR3B</italic>, <italic>PIK3C3</italic>, <italic>TOPORS</italic>, <italic>FASTKD3</italic>, <italic>CYPLP1A1</italic>, and <italic>UACA</italic>. Our results throw light on the nature of the natural selection of <italic>S. caldwelli</italic> and contribute to future immunological and transcriptome studies.</p>