Comparative Transcriptome Analysis of Testes and Ovaries Reveals Sex-Biased Gene Expression in Adult Mud Carp (Cirrhinus molitorella)

Adult gonadal transcriptomes reflect tissue specialization and reproductive activity. We compared testes and ovaries from seven male and seven female mud carp (Cirrhinus molitorella) and evaluated the results in an independent six-fish public cohort and by RT-qPCR in a further 12 fish. DESeq2 analysis identified 12,757 sex-biased loci among 19,322 tested loci, comprising 8213 testis-biased and 4544 ovary-biased loci. Testis-biased loci were enriched for cilium and axoneme assembly, whereas ovary-biased loci were enriched for RNA processing and ribosome biogenesis. In a common-reference comparison with the public cohort, 9045 of 9104 shared differentially expressed loci (99.4%) had concordant directions, and fold changes across 17,283 loci were strongly correlated (Pearson r = 0.917). RT-qPCR of seven candidate genes reproduced the RNA-seq direction in all cases, six of them significantly, and RT-qPCR and RNA-seq fold changes were closely correlated (r = 0.984). Protein phylogeny and local synteny reassigned two strongly testis-biased loci originally annotated as foxl2 and wnt4a to foxl2l-like and wnt4b-like paralogues. Differential splicing analysis identified 923 skipped-exon and mutually exclusive-exon events across 743 loci. These results provide a validated set of sex-biased genes and refined paralogue annotations for future studies of reproduction and sex control in mud carp.