Integrated Transcriptome Landscape of mRNAs, lncRNAs, circRNAs, and miRNAs Reveals Molecular Regulatory Networks of Sex Differentiation in the Zig-Zag Eel (Mastacembelus armatus)

The zig-zag eel (Mastacembelus armatus) exhibits sexual dimorphism in growth patterns. Identifying the genes involved in sex differentiation is a crucial step toward achieving single-sex breeding and serves as a vital foundation for elucidating the XY sex determination mechanism in M. armatus. This study measured the morphological characteristics of male and female M. armatus and found that males were significantly superior to females in body weight and nearly all morphological indices. Subsequently, whole-transcriptome sequencing was performed on the gonads of adult males and females, identifying 11,714 DEmRNAs, 3442 DElncRNAs, 416 DEcircRNAs, and 620 DEmiRNAs, including male sex differentiation genes such as Sox30, Tbx1, Sox9, and Gata4, and female sex differentiation genes like Sox3, Foxl2, and Wnt4a. Functional enrichment analysis identified pathways associated with sex differentiation, including the TGF-beta signaling pathway, the steroid hormone biosynthesis, the Hippo signaling pathway, and the Wnt signaling pathway, etc. A ceRNA network was constructed based on differentially expressed mRNAs and ncRNAs, revealing that the sex differentiation-related genes Sox3, Sox9, Sox30, Tbx1, and Wt1 are regulated by one or multiple pairs of lncRNA/circRNA-miRNA pairs. The study results will provide molecular targets for research on sex-controlled breeding in M. armatus and lay an important theoretical foundation for clarifying its sex differentiation mechanisms.