Abstract
BackgroundSex 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.ResultsUsing 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.ConclusionsWe 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.
Highlights
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
A wide variety of genetic sex-determining mechanisms have been identified in teleost species, with various genes serving as the “master sex-determining genes” such as DMRT1 in medaka species Oryzias latipes and O. curvinotus [8, 9], GSDF in the medaka species Oryzias luzonensis [10], SDY in rainbow trout (Oncorhynchus mykiss) [11], (2019) 17:6 and AMHY in the Patagonian pejerrey (Odontesthes hatcheri) [12]
A large number of individuals were analyzed to reduce the area of the sex determination locus to a small genomic region which was located on the X and Y chromosome-specific sequence assemblies
Summary
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. Analysis of sex determination patterns in half-smooth tongue sole (Cynoglossus semilaevis) revealed that this species has a ZW type sex determination system, and that the dmrt gene exhibited characteristics of sex-determining genes such as sex chromosome linkage, male-specific expression, and essentiality for testis development [14], and that its knockout in ZZ fish (male karyotype) led to the development of female phenotypes [15]. Even though genetic studies can clearly map the sex determination gene to a chromosomal region, identification of sex determination gene is still a daunting task with teleost fish
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