Integrated landscape of accessible regions and transcriptomic profiles in Penaeus monodon during ovarian maturation

The ovary maturation process poses a significant constraint on the commercial production and breeding of Penaeus monodon, one of the most extensively cultivated crustacean species. The reproductive stage is controlled by neuropeptide hormones and various proteins released from secretory sites (X-organ/sinus gland, XO/SG) within the eyestalk. Unilateral eyestalk ablation has been a widely employed method to artificially induce ovarian maturation in farmed P. monodon. To better understand the reproductive regulation mechanism in P. monodon, we have investigated the both the transcriptomes and regulatory mechanisms of the eyestalk ablated ovary developmental stages with RNA-seq and ATACseq. For RNA-seq data, a total of 182.29 G of clean data was obtained, with the effective data distribution for each sample ranging from 6.42 to 7.04 G. Meanwhile, the differentially expressed genes (DEGs) between ovarian development stages were identified. We examined, through DEG enrichment analysis, eyestalk gene expression patterns for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We also identified a variety of accessible regions that appear to be differentially expressed throughout ovarian maturation. These include Motifs that encode bZIP and C2H2 transciption factor families. Furthermore, by integrating DEGs and differential accessible regions, we found HIF-signaling pathway, AGE-RAGE signaling pathway, ABC transporters pathways, were involved during ovarian maturation. Our study offers new insights into the role of the eyestalk in the regulation of reproduction, providing a basis for selective breeding and exploring alternative methods to induce ovary maturation.