Table6_Identification of Potential Blind-Side Hypermelanosis-Related lncRNA–miRNA–mRNA Regulatory Network in a Flatfish Species, Chinese Tongue Sole (Cynoglossus semilaevis).xlsx

Blind-side hypermelanosis has emerged as a major concern in commercial rearing environments of the flatfish aquaculture industry. To date, the underlying molecular mechanisms are not well understood. To fill this gap, in this study, whole transcriptomic sequencing and analyses were performed using normal skins and hypermelanic skins of the blind side of Chinese tongue sole (Cynoglossus semilaevis). Differentially expressed long non-coding RNAs (DElncRNAs), miRNAs (DEmiRNAs), and differentially expressed genes as well as their competing endogenous RNA (ceRNA) networks were identified. A total of 34 DElncRNAs, 226 DEmiRNAs, and 610 DEGs were identified. Finally, lncRNA–miRNA–mRNA regulatory networks (involving 29 DElncRNAs, 106 DEmiRNAs, and 162 DEGs) associated with blind-side hypermelanosis were constructed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of 162 DEGs in ceRNA networks identified DEGs (e.g., oca2, mc1r, and ihhb) in pigmentation-related biological processes and DEGs (e.g., ca4, glul, and fut9) in nitrogen metabolism, glycosphingolipid biosynthesis, and folate biosynthesis pathways, as well as their corresponding DElncRNAs and DEmiRNAs to potentially play key regulatory roles in blind-side hypermelanosis. In conclusion, this is the first study on the ceRNA regulatory network associated with blind-side hypermelanosis in flatfish. These new findings expand the spectrum of non-coding regulatory mechanisms underpinning blind-side hypermelanosis, which facilitates the further exploration of molecular regulatory mechanisms of malpigmentation in flatfish.

盲侧黑色素沉着过度症（blind-side hypermelanosis）已成为比目鱼（flatfish）养殖业商业化养殖环境中的主要关切问题。迄今为止，其潜在分子机制尚未得到充分阐释。为填补这一研究空白，本研究以半滑舌鳎（Cynoglossus semilaevis）盲侧的正常皮肤与异常黑色素沉着皮肤为材料，开展了全转录组测序与分析工作。本研究鉴定得到了差异表达长链非编码RNA（differentially expressed long non-coding RNAs, DElncRNAs）、差异表达miRNA（differentially expressed miRNAs, DEmiRNAs）、差异表达基因（differentially expressed genes, DEGs）及其内源竞争RNA（competing endogenous RNA, ceRNA）调控网络，共计鉴定得到34个DElncRNAs、226个DEmiRNAs以及610个DEGs。最终，本研究构建了与盲侧黑色素沉着过度症相关的lncRNA-miRNA-mRNA调控网络，该网络涵盖29个DElncRNAs、106个DEmiRNAs以及162个DEGs。本研究对ceRNA网络中的162个DEGs开展了基因本体（Gene Ontology, GO）富集分析与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）富集分析，鉴定得到了与色素沉着相关生物学过程相关的DEGs（如oca2、mc1r及ihhb），以及参与氮代谢、糖鞘脂生物合成与叶酸生物合成通路的DEGs（如ca4、glul及fut9），同时明确了其对应的DElncRNAs与DEmiRNAs可能在盲侧黑色素沉着过度症中发挥关键调控作用。综上，本研究是首个针对比目鱼盲侧黑色素沉着过度症相关ceRNA调控网络的研究。本研究新发现拓展了盲侧黑色素沉着过度症背后的非编码调控机制谱系，为进一步探究比目鱼色素异常的分子调控机制提供了重要支撑。