Li Ziming, Liu Xinghai, Tang Xinyue, Yang Yujia
The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
Comp Biochem Physiol Part D Genomics Proteomics. 2025 Jun;54:101396. doi: 10.1016/j.cbd.2024.101396. Epub 2024 Dec 9.
Apostichopus japonicus is a representative temperate sea cucumber species, that mainly inhabits in coastal zone of the continental shelf. With high nutritional value and important medical value, A. japonicus become an important commercial aquaculture species and produce significant economic value in recent years. A. japonicus has no sexual dimorphism that can be used to distinguish female and male individuals by external appearance and morphology. The phenotype sex can be only detected by dissecting and observing gonad tissue, thus the breeding efficiency could be greatly reduced. This limitation has hindered the advancement of selective breeding programs and sea cucumber industry. To investigate the genetic basis of reproductive biology in A. japonicus, advanced sequencing techniques, such as next- and third-generation sequencing, have been employed to explore the roles of non-coding RNAs and other genetic factors, offering new insights into sex determination mechanisms. To further gain a deeper understanding of the knowledge underlying lncRNAs in gonadal differentiation, we conducted a comparative transcriptome sequencing analysis of gonadal tissues from both sexes. In our research, a total of 3990 novel lncRNAs and 1441 differentially expressed lncRNAs were identified between female and male gonads. Additionally, a molecular regulatory network indicating lncRNA-mRNA interactions was constructed based on transcriptional profiles, which provide insights into the potential cis- and trans- target genes of lncRNAs. The gonadal transcriptome analysis identified a number of novel long non-coding RNAs involved in female and male reproduction process. Both cis- and trans-acting regulatory networks indicating lncRNA-mRNA interaction were constructed based on transcriptional profiles. These findings provide new insights into the lncRNA-mediated regulation of reproductive biology in marine invertebrates, indicating the crucial roles of long non-coding sequences in regulating expression profiles. Further, the GO and KEGG enrichment analyses of cis- and trans- targeted mRNA for differentially expressed lncRNA indicated that sexual reproduction (GO:0019953), germ cell development (GO:0007281), and negative regulation of hormone secretion (GO:0046888) are potentially involved in gonadal differentiation through the regulation of long non-coding sequences. Notably, besides the classical reproduction related signaling pathway like Gonadotropin-releasing hormone (GnRH) secretion (ko04929), several regulatory pathways, such as Epidermal growth factor receptor (ErbB) signaling pathway (ko04012), TGF-beta signaling pathway (ko04350), and neurotrophin signaling pathway (ko04722) were also enriched and potentially involved in sex differentiation and gonadal development.
刺参是一种典型的温带海参物种，主要栖息于大陆架沿海区域。刺参具有较高的营养价值和重要的医学价值，近年来已成为重要的商业养殖品种并产生了显著的经济价值。刺参不存在可通过外观和形态来区分雌雄个体的性别二态性。只能通过解剖和观察性腺组织来检测表型性别，因此繁殖效率可能会大大降低。这一限制阻碍了选择性育种计划和海参产业的发展。为了研究刺参生殖生物学的遗传基础，已采用先进的测序技术，如下一代测序和第三代测序，来探索非编码RNA和其他遗传因素的作用，为性别决定机制提供了新的见解。为了进一步深入了解性腺分化中lncRNA的相关知识，我们对雌雄两性的性腺组织进行了比较转录组测序分析。在我们的研究中，在雌性和雄性性腺之间共鉴定出3990个新的lncRNA和1441个差异表达的lncRNA。此外，基于转录谱构建了一个指示lncRNA-mRNA相互作用的分子调控网络，这为lncRNA的潜在顺式和反式靶基因提供了见解。性腺转录组分析鉴定出了一些参与雌雄生殖过程的新的长链非编码RNA。基于转录谱构建了指示lncRNA-mRNA相互作用的顺式和反式作用调控网络。这些发现为海洋无脊椎动物中lncRNA介导的生殖生物学调控提供了新的见解，表明长链非编码序列在调节表达谱中起着关键作用。此外，对差异表达lncRNA的顺式和反式靶向mRNA的GO和KEGG富集分析表明，有性生殖（GO:0019953）、生殖细胞发育（GO:0007281）和激素分泌的负调控（GO:0046888）可能通过长链非编码序列的调控参与性腺分化。值得注意的是，除了像促性腺激素释放激素（GnRH）分泌（ko04929）这样的经典生殖相关信号通路外，表皮生长因子受体（ErbB）信号通路（ko04012）、转化生长因子-β信号通路（ko04350）和神经营养因子信号通路（ko04722）等一些调控通路也被富集并可能参与性别分化和性腺发育。
