AUTHOR=Li Ruihan , Wang Xiaoai , Bian Chao , Gao Zijian , Zhang Yuanwei , Jiang Wansheng , Wang Mo , You Xinxin , Cheng Le , Pan Xiaofu , Yang Junxing , Shi Qiong 

TITLE=Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes

JOURNAL=Frontiers in Genetics

VOLUME=Volume 12 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.736500

DOI=10.3389/fgene.2021.736500

ISSN=1664-8021

ABSTRACT=<p>An adult <italic>Sinocyclocheilus maitianheensis</italic>, a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were annotated. Based on a comparative phylogenetic analysis of five <italic>Sinocyclocheilus</italic> species and other five representative vertebrates with published genome sequences, we found that <italic>S. maitianheensis</italic> is close to <italic>Sinocyclocheilus anophthalmus</italic> (a cave-restricted species with similar locality). Moreover, the assembled genomes of <italic>S. maitianheensis</italic> and other four <italic>Sinocyclocheilus</italic> counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted <italic>Sinocyclocheilus</italic> species. In summary, we report the first genome assembly of <italic>S. maitianheensis</italic>, which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish.</p>