Data underlying the publication: miRNA and mRNA integrated analysis reveal differential expression genes in the gonad of sea cucumber Holothuria leucospilota

MicroRNAs are defined as a class of short noncoding RNAs, which play important function in cell differentiation, developmental process and gender determination. The sea cucumber <em>Holothuria leucospilota</em> is a member of the Echinodermata, known for its excellent nutritional and economic value. Breeding efficiency of sea cucumbers is low due to the difficulty in distinguishing between male and female individuals. Discovering molecular markers that distinguish between genders will provide a robust strategy for elucidating the genetic mechanisms governing gender determination and differentiation. In this investigation, high-throughput sequencing was utilized to compare miRNA expression patterns in the gonadal tissues of male and female specimens of <em>Holothuria leucospilota</em>. A total of 584 known miRNAs and 404 novel miRNAs were identified, of which 97 miRNAs were identified as significantly differentially expressed miRNAs (DEMs) between male and female sea cucumbers. These findings enabled the construction of a miRNA-mRNA regulatory network. Pathway analysis of target genes highlighted the potential roles of neuroactive ligand-receptor interactions, calcium signaling, Salmonella infection, endocytosis, and MAPK signaling in governing gener differentiation processes. The expression results of high-throughput sequencing were validated in sc-miR121, sc-miR41, sc-miR67, sc-miR90, sc-miR104 and sc-miR189 by quantitative real-time quantity polymerase chain reaction (RT-qPCR). In summary, our results will provide a foundation for future studies of miRNA regulation in gender differentiation of sea cucumber <em>H. leucospilota</em>.

微小RNA（microRNAs）是一类短链非编码RNA，在细胞分化、发育进程及性别决定过程中发挥重要功能。黑乳海参（Holothuria leucospilota）为棘皮动物门物种，兼具优异的营养与经济价值。由于难以区分雌雄个体，海参的繁育效率普遍偏低。发掘可区分性别的分子标记，将为阐明调控性别决定与分化的遗传机制提供稳健的研究策略。本研究采用高通量测序技术，对比分析了黑乳海参（Holothuria leucospilota）雌雄个体性腺组织的miRNA表达谱。共鉴定得到584个已知微小RNA与404个新型微小RNA，其中97个为雌雄海参间显著差异表达的微小RNA（differentially expressed miRNAs, DEMs）。基于上述研究结果构建了miRNA-mRNA调控网络。对靶基因的通路分析显示，神经活性配体-受体相互作用、钙信号通路、沙门氏菌感染、内吞作用以及丝裂原活化蛋白激酶（MAPK）信号通路在调控性别分化过程中具有潜在作用。随后通过实时定量聚合酶链反应（quantitative real-time polymerase chain reaction, RT-qPCR）验证了sc-miR121、sc-miR41、sc-miR67、sc-miR90、sc-miR104及sc-miR189的表达结果。综上，本研究结果将为后续黑乳海参（H. leucospilota）性别分化相关miRNA调控研究奠定基础。