Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation

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.

The regulation mechanism of lncRNAs and mRNAs in sea cucumbers under global climate changes: Defense against thermal and hypoxic stresses

“…A. japonicus is a good model holothurian species, because of its economic and ecological value. LncRNAs of A. japonicus have fewer exons and shorter transcripts in length compared with mRNAs, and these results are in agreement with those of previous studies examining pig (Wang et al, 2016), rat (Wang et al, 2014) and oyster (Feng et al, 2018). With the absence of lncRNA data for other holothurians, the conservation of lncRNAs is difficult to properly evaluate in sea cucumbers.…”

“…However, the regulatory mechanisms remain unclear, especially in sea cucumber. To date, many lncRNAs have been identified in model animals including human (Wapinski and Chang, 2011), rat (Wang et al, 2014), zebrafish (Pauli et al, 2012), arabidopsis (Liu et al, 2012), fruit fly (Nyberg and Machado, 2016), and elegans (Nam and Bartel, 2012); they have also been identified in other vertebrates, such as pig (Wang et al, 2016) and chicken (Li et al, 2012); and other marine animals, such as oyster (Feng et al, 2018) and salmon (Valenzuela-Miranda and Gallardo-Escárate, 2016). However, information concerning the systematic identification and function of lncRNAs in marine invertebrates remains lacking, especially for echinoderms.…”

Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity

“…Previous experimental crosses have shown that shell color has a genetic basis in the Manila clam (Peignon et al., 1995). Color is one of the most conspicuous phenotypic traits in R. philippinarum , and the diverse colors of molluscan shells are generally believed to be determined by the presence of biological pigments (Mann and Jackson, 2014, Lemer et al., 2015, Feng et al., 2018). Several studies have been conducted of the physiological, biochemical, and molecular responses to different types of biotic and abiotic stress in different shell color strains of the Manila clam (Zhang and Yan, 2010, Nie et al., 2017a, Nie et al., 2017b).…”

Identification of Immune Response to Sacbrood Virus Infection in Apis cerana Under Natural Condition

“…protein DDB_G0277255-like, were significantly down-regulated (P < 0.01). LOC410515 may have a similar function in immune with a homologous protein, Apis dorsata chorion peroxidase-like (XP_006611124.1) (NCBI blast sequence identify >75%), which played an important role in melanin synthesis (Feng et al, 2018).…”