Characterization of the Mantle Transcriptome of Yesso Scallop (Patinopecten yessoensis): Identification of Genes Potentially Involved in Biomineralization and Pigmentation

Abstract

The Yesso scallop Patinopecten yessoensis is an economically important marine bivalve species in aquaculture and fishery in Asian countries. However, limited genomic resources are available for this scallop, which hampers investigations into molecular mechanisms underlying their unique biological characteristics, such as shell formation and pigmentation. Mantle is the special tissue of P. yessoensis that secretes biomineralization proteins inducing shell deposition as well as pigmentation on the shells. However, a current deficiency of transcriptome information limits insight into mechanisms of shell formation and pigmentation in this species. In this study, the transcriptome of the mantle of P. yessoensis was deeply sequenced and characterized using Illumina RNA-seq technology. A total of 86,521 unique transcripts are assembled from 55,884,122 reads that passed quality filters, and annotated, using Gene Ontology classification. A total of 259 pathways are identified in the mantle transcriptome, including the calcium signaling and melanogenesis pathways. A total of 237 unigenes that are homologous to 102 reported biomineralization genes are identified, and 121 unigenes that are homologous to 93 known proteins related to melanin biosynthesis are found. Twenty-three annotated unigenes, which are mainly homologous to calmodulin and related proteins, Ca2+/calmodulin-dependent protein kinase, adenylate/guanylate cyclase, and tyrosinase family are potentially involved in both biomineralization and melanin biosynthesis. It is suggested that these genes are probably not limited in function to induce shell deposition by calcium metabolism, but may also be involved in pigmentation of the shells of the scallop. This potentially supports the idea that there might be a link between calcium metabolism and melanin biosynthesis, which was previously found in vertebrates. The findings presented here will notably advance the understanding of the sophisticated processes of shell formation as well as shell pigmentation in P. yessoensis and other bivalve species, and also provide new evidence on gene expression for the understanding of pigmentation and biomineralization not only in invertebrates but also probably in vertebrates.

Lethal and sublethal responses of native mussels (Unionidae: Lampsilis siliquoidea and Lampsilis higginsii) to elevated carbon dioxide

“…Calmodulin (CAL) is a multifunctional calciumbinding messenger protein that mediates many fundamental cellular processes. In bivalves, CAL is integral to Ca 2+ uptake from the water by the gills and for shell formation and biomineralization (Ren et al 2013;Liu et al 2015;Sun et al 2015). Na+/K+ ATPase is critical to active transport and as secondary transport of other ions and organic molecules (Giacomin et al 2013); it may play a role in reducing acidosis by excretion of NH 4 + from the mantle (Hüning et al 2013).…”

Transcriptome survey of phototransduction and clock genes in marine bivalves

“…Mixed samples of mantle tissue from six scallops of Patinopecten yessoensis produced a total of 55.9 million reads using Illumina paired-end sequencing (Sun et al, 2015), which were used in this study. The raw data are available online at the Short Read Archive of the National Center for Biotechnology Information's (NCBI) trace archive (GenBank accession No.…”

“…SRP046039). The sequencing data were filtered and assembled as described previously (Sun et al, 2015). Gene expression data for mantle tissue of the Pacific oyster, Crassostrea gigas, were available from Zhang et al (2012) and was downloaded from an online resource (http://www.oysterdb.com/).…”

“…All unigenes from KEGG pathways of phototransduction and the circadian clock were selected and identified as candidate genes. Second, the unigenes were submitted to BLAST with annotation against NCBI non-redundant protein sequences (Nr) and nonredundant nucleotide sequences (Nt) to arrange transcripts into clusters according to sequence similarities in order to obtain significant annotations (Sun et al, 2015). Identification of phototransduction and circadian genes was further carried out by searching for key words of genes reported in terrestrial species, such as arrestin, calmodulin, guanyl cyclase, inaC, opsin, phosducin, recoverin, clock, period, timeless, and cycle (Table S1).…”

“…As a high-throughput method for transcriptome sequencing, RNA-Seq has been widely applied to uncover genes central to the circadian clock at the transcriptome level (Vize, 2009;Pairett and Serb, 2013;Shoguchi et al, 2013). To explore the potential genes underlying biological rhythms in marine species and investigate how these genes are correlated with terrestrial models, we made use of the recent generation of a large expressed sequence tag (EST) dataset developed from the mantle transcriptomes of marine bivalves (Pairett and Serb, 2013;Sun et al, 2015). The analysis allowed us to identify most of the key circadian genes from insects and mammals in the transcriptomes of marine bivalves, which indicated that many of these genes are very highly conserved in the animal kingdom.…”