Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and have drawn extensive attention in the past few years. However, lncRNAs remain poorly understood about expression and roles in Crassostrea gigas, a potential model organism for marine molluscan studies. Here, we systematically identified lncRNAs in the mantles of C. gigas from four full-sib families characterized by white, black, golden, and partially pigmented shell. Using poly(A)-independent and strand-specific RNA-seq, a total of 441,205,852 clean reads and 12,243 lncRNA transcripts were obtained. LncRNA transcripts were relatively short with few exons and low levels of expression in comparison to protein coding mRNA transcripts. A total of 427 lncRNAs and 349 mRNAs were identified to differentially express among six pairwise groups, mainly involving in biomineralization and pigmentation through functional enrichment. Furthermore, a total of 6 mRNAs and their cis-acting lncRNAs were predicted to involve in synthesis of melanin, carotenoid, tetrapyrrole, or ommochrome. Of them, chorion peroxidase and its cis-acting lincRNA TCONS_00951105 are implicated in playing an essential role in the melanin synthetic pathway. Our studies provided the first systematic characterization of lncRNAs catalog expressed in oyster mantle, which may facilitate understanding the molecular regulation of shell colour diversity and provide new insights into future selective breeding of C. gigas for aquaculture.
Highlights
The large proportion of a eukaryotic genome is transcribed to produce a huge array of RNA molecules differing in protein-coding capability, size, and abundance[1]
This study provided a catalog of Long non-coding RNAs (lncRNAs) in mantle of five-month-old Pacific oysters and profiled their expression in four shell colours variants
We identified a total of 12,443 lncRNAs, encoded by 11,637 gene loci, consisting of 8,226 lincRNAs, 387 antisense lncRNAs, and 3,630 intronic lncRNAs
Summary
The large proportion of a eukaryotic genome is transcribed to produce a huge array of RNA molecules differing in protein-coding capability, size, and abundance[1]. Characterization of the shell pigments and identification of molecular pathways involved in their synthesis in Mollusca lag behind the large numbers of studies undertaken on plants, vertebrates and insects[12,13,14,15,16,17]. The regulatory mechanism for melanin synthesis is better known in cephalopods, involving in the activation of tyrosinase and increased melanin synthesis in the ink gland[25] It is noteworthy, some of the shell pigments have been shown to be produced via the highly conserved pathways. The recently released genome sequence of C. gigas enabled us to develop a pipeline to identify 11,668 long intergenic non-coding RNAs (lincRNAs) from different tissues and developmental stages, based on RNA-seq resources available[2]. The whole lncRNAs catalog of C. gigas is not well characterized in any tissue, let alone their association with pigmentation
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