Multi-omics integration identifies diverse transcripts and chromatin accessibility profiles in Monopterus albus gonads

The swamp eel (Monopterus albus) is an economically important freshwater fish. However, its natural sex reversal contributes to low egg production and fry shortages in aquaculture. The molecular mechanisms governing this process remain poorly understood, hindered by incomplete gene annotations and a lack of comprehensive multi-omics characterization of the gonad. To address this, we performed integrated Iso-seq, RNA-seq, and ATAC-seq profiling across nine key stages of natural female-to-male sex reversal. This approach revealed an extensive, previously unannotated transcriptome landscape, identifying 37,911 novel transcripts. These included 16,900 novel genes and alternative isoforms derived from 24,193 annotated genes. Furthermore, chromatin accessibility mapping identified 2,174 putative cis-regulatory elements, uncovering dynamic regulatory shifts correlated with gene expression changes during sex reversal. Our integrated multi-omics analysis delivers a significantly enhanced transcript annotation framework for M. albus, resolving precise polyadenylation sites and surpassing the current NCBI annotation in comprehensiveness. Collectively, this work establishes an essential resource for investigating gonadal development and deciphering sex reversal mechanisms in fish.