Transcription Analysis for Core Networks of lncRNAs–mRNAs: Implication for Potential Role in Sterility of Crassostrea gigas

Abstract

Long noncoding RNA (lncRNA), a type of non-protein-coding transcript, is emerging as a crucial regulator of gene expression. However, few roles of lncRNA in the reproductive process of the Pacific oyster (Crassostrea gigas) have been defined, especially in the regulatory mechanism of sterile triploids gametogenesis. To uncover the potential role of lncRNA, the gonads of diploids, sterile triploids, and partially sterile triploids underwent RNA sequencing. A total of 9618 reliable lncRNAs were identified. The target relationship between lncRNA and mRNA was predicted based on cis, trans, and antisense regulation with bioinformatic software. We chose differentially expressed lncRNAs and mRNAs when sterile triploids were compared to partially sterile triploids and diploids for subsequent functional enrichment analysis. Findings revealed that trans-regulatory lncRNAs might play a significant role in the gametogenesis of C. gigas. Combining pathway results, we constructed core networks of lncRNAs–mRNAs for triploid sterile females and hermaphrodites. Fifty-four genes related to cell division, germline-cell maintenance, and glycogen metabolism were found to be associated with sterility. A total of 28 candidate lncRNAs were predicted to trans-regulate these genes. We speculated that MSTRG.79882.3 and MSTRG.79882.4 for triploid sterile females and MSTRG.33704.1, MSTRG.63844.1, and MSTRG.5675.1 for hermaphrodites were highly important as they were predicted to regulate more sterility-specific genes than others. Our work collectively identified sterility-related lncRNAs and implicated the potential mechanism of lncRNA-mediated regulation in the gametogenesis of sterile triploid oysters.

Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora

“…Here, over 88% of P. yessoensis lncRNAs were novel identified, which had no orthologs in other species. High ratio of novel lncRNAs were also found in other marine organism, for example, 98% lncRNAs identified in the spleen of the flounder ( Paralichthys olivaceus ) were unknown [ 68 ], and lncRNAs obtained in the gonad of the Pacific oyster were all novel [ 40 ]. Though the lncRNA resources in molluscs are still limited, the high ratio of unknown lncRNAs found in this study approved the view that majority of lncRNAs were short of primary sequence conservation [ 24 , 68 ].…”

“…LncRNAs exhibit crucial effects on diverse biological processes in vertebrates, such as reproduction, development, metabolism, immunity, sex determination and differentiation and so on [ 28 – 33 ]. With the prevalence of the next-generation sequencing, characterizations and expression patterns of lncRNAs in molluscs have been gradually investigated, and they are found functioning in diverse bioprocesses, covering immune and stress response [ 34 – 38 ], muscle growth [ 39 ], gametogenesis [ 40 ] and larval development [ 41 ]. Emerging evidence has also revealed that lncRNAs are involved in the modulation of shell biomineralization and pigmentation in molluscs [ 42 – 46 ].…”