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

Yangzhen Li,Yuanri Hu,Peng Cheng,Songlin Chen

doi:10.3389/fgene.2021.817117

Abstract

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.

Highlights

Chinese tongue sole (Cynoglossus semilaevis) is a prevalent flatfish species in Chinese aquaculture because of its superior nutritive value and economic significance
To gain an overview of small RNA (sRNA) of blind-side hypermelanotic and normal skin samples and to identify miRNAs that are potentially involved in blind side hypermelanosis mechanisms, six sRNA and six strand-specific libraries were separately constructed by using BH and BN samples, which were sequenced based on Illumina sequencing technology
Based on the position of these novel lncRNAs in the genome relative to protein-coding genes, they were divided into five categories, including 340 sense lncRNAs, 1734 antisense lncRNAs, 145 intronic lncRNAs, 276 bidirectional lncRNAs, and 2079 intergenic lncRNAs (Figure 1C)

Summary

Introduction

Chinese tongue sole (Cynoglossus semilaevis) is a prevalent flatfish species in Chinese aquaculture because of its superior nutritive value and economic significance. Tongue sole will undergo morphological metamorphosis with an asymmetrical body plan during the larval stage to adapt to an over-substrate dwelling (benthic) lifestyle in later developmental stages (Chen et al, 2014; Shao et al, 2017; Fox et al, 2018; Lü et al, 2021). After metamorphosis, both eyes move to the same side (i.e., the ocular side), which becomes pigmented (black brown) while the blind side remains unpigmented (pure white) (Kang et al, 2011). The proportion of hypermelanic individuals within aquaculture populations reaches as much as 90% (range 10–90%), resulting in a 10–15% drop of the market price (Li et al, 2021b)

Methods

Results

Discussion

Conclusion