An integration analysis of whole transcriptome sequencing of gonads and genome-wide identification of ovary- and testis-biased genes and microRNAs in Apostichopus japonicus. This study investigates hub genes and pathways, and molecular networks between protein-coding genes and non-coding microRNAs and provides insights into the potential role of microRNAs in reproductive biology and regulatory mechanisms on gonadal differentiation in marine invertebrates.