The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish

• Published in: BMC biology 2019-01, Vol.17 (1), p.6-6, Article 6
• Main Authors: Bao, Lisui, Tian, Changxu, Liu, Shikai, Zhang, Yu, Elaswad, Ahmed, Yuan, Zihao, Khalil, Karim, Sun, Fanyue, Yang, Yujia, Zhou, Tao, Li, Ning, Tan, Suxu, Zeng, Qifan, Liu, Yang, Li, Yueru, Li, Yun, Gao, Dongya, Dunham, Rex, Davis, Kenneth, Waldbieser, Geoffrey, Liu, Zhanjiang
• Format: Article
• Language: English
• Subjects: Alternative splicing; Analysis; Animals; Birds; Breast cancer; Catfish; Chromosome Mapping; Chromosomes; DNA sequencing; Female; Females; Fish; Fishes; Gene expression; Gene sequencing; Genes; Genetic analysis; Genetic distance; Genetic Linkage; Genetic research; Genome; Genomes; Genomics; Ictaluridae - genetics; Male; Males; Nucleotide sequence; PacBio; Recombination; Ribonucleic acid; RNA; RNA sequencing; RNA-Seq; Sequence Analysis, DNA; Sex; Sex chromosomes; Sex determination; Sex determination (Diagnosis); Sex determination (Genetics); Sex Determination Processes - genetics; Sex differentiation; Sexes; Vertebrates; Y Chromosome; Y chromosomes
• ISSN: 1741-7007; 1741-7007
• DOI: 10.1186/s12915-019-0627-7

Sex determination mechanisms in teleost fish broadly differ from mammals and birds, with sex chromosomes that are far less differentiated and recombination often occurring along the length of the X and Y chromosomes, posing major challenges for the identification of specific sex determination genes. Here, we take an innovative approach of comparative genome analysis of the genomic sequences of the X chromosome and newly sequenced Y chromosome in the channel catfish. Using a YY channel catfish as the sequencing template, we generated, assembled, and annotated the Y genome sequence of channel catfish. The genome sequence assembly had a contig N50 size of 2.7 Mb and a scaffold N50 size of 26.7 Mb. Genetic linkage and GWAS analyses placed the sex determination locus within a genetic distance less than 0.5 cM and physical distance of 8.9 Mb. However, comparison of the channel catfish X and Y chromosome sequences showed no sex-specific genes. Instead, comparative RNA-Seq analysis between females and males revealed exclusive sex-specific expression of an isoform of the breast cancer anti-resistance 1 (BCAR1) gene in the male during early sex differentiation. Experimental knockout of BCAR1 gene converted genetic males (XY) to phenotypic females, suggesting BCAR1 as a putative sex determination gene. We present the first Y chromosome sequence among teleost fish, and one of the few whole Y chromosome sequences among vertebrate species. Comparative analyses suggest that sex-specific isoform expression through alternative splicing may underlie sex determination processes in the channel catfish, and we identify BCAR1 as a potential sex determination gene.