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

Area of Science:

• Aquaculture
• Genomics
• Developmental Biology

Background:

• The swamp eel (Monopterus albus) is vital for aquaculture, but natural sex reversal causes low egg production.
• Understanding the molecular basis of this sex reversal is crucial for improving aquaculture yields.
• Current knowledge is limited by incomplete gene annotations and a lack of multi-omics data.

Purpose of the Study:

• To comprehensively characterize the transcriptome and epigenome during Monopterus albus sex reversal.
• To identify novel genes, transcripts, and regulatory elements involved in gonadal development.
• To establish an enhanced annotation framework for Monopterus albus.

Main Methods:

• Integrated Iso-seq, RNA-seq, and ATAC-seq profiling across nine developmental stages.
• Analysis of chromatin accessibility and gene expression dynamics.
• Comparative analysis with existing NCBI annotations.

Main Results:

• Identification of 37,911 novel transcripts, including 16,900 novel genes and alternative isoforms.
• Discovery of 2,174 putative cis-regulatory elements with dynamic accessibility shifts.
• Development of a significantly improved and comprehensive transcript annotation for Monopterus albus.

Conclusions:

• This multi-omics dataset provides an essential resource for studying fish gonadal development.
• The findings offer insights into the molecular mechanisms underlying sex reversal in Monopterus albus.
• The enhanced annotation framework will facilitate future research in fish reproduction and aquaculture.