Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX

Abstract

BackgroundBivalves comprise 30,000 extant species, constituting the second largest group of mollusks. However, limited genetic research has focused on this group of animals so far, which is, in part, due to the lack of genomic resources. The advent of high-throughput sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provides a turning point for bivalve research. In the present study, we performed de novo transcriptome sequencing to first produce a comprehensive expressed sequence tag (EST) dataset for the Yesso scallop (Patinopecten yessoensis).ResultsIn a single 454 sequencing run, 805,330 reads were produced and then assembled into 32,590 contigs, with about six-fold sequencing coverage. A total of 25,237 unique protein-coding genes were identified from a variety of developmental stages and adult tissues based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified. More than 49,000 single nucleotide polymorphisms (SNPs) and 2,700 simple sequence repeats (SSRs) were also detected.ConclusionOur data provide the most comprehensive transcriptomic resource currently available for P. yessoensis. Candidate genes potentially involved in growth, reproduction, and stress/immunity-response were identified, and are worthy of further investigation. A large number of SNPs and SSRs were also identified and ready for marker development. This resource should lay an important foundation for future genetic or genomic studies on this species.

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana

“…This final dataset was then subjected to putative functional annotation using a more rigorous blastx search (E value < 10 -10 ) against the NCBI non-redundant (nr) protein database. The length of contigs was significantly correlated with the number of sequences assembled into them (Pearson ρ = 0.53; n= 20,938; p < 0.0001), as expected for 454 reads (Parchman et al, 2010) and the size distribution of contigs resembled that of previous 454 studies (Bettencourt et al, 2010;Fraser et al, 2011;Hou et al, 2011) (Supplementary Figures S1A and S1B). Files containing the reads have been submitted to the National Center for Biotechnology Information Short Read Archive [GenBank: SRX790900].…”

“…The number of pathways identified in this study is superior to other previous studies (i.e. Hao et al, 2011;Hou et al, 2011) and might suggest that the C. brasiliana sequence data contain a large diversity of genes involved in a variety of biological processes, and do not contain notable biases towards particular categories of genes. Of these 276 KEGG pathways, those commonly related to xenobiotic biotransformation and response to stress in aquatic organisms were represented by sequences classified into "metabolism of xenobiotics by cytochrome P450", "drug metabolismcytochrome P450", "drug metabolism -other enzymes", "glutathione metabolism", and "pentose phosphate pathway".…”

“…9.9% in the razor clam Sinonovacula constricta (Niu et al, 2013), 12% in the blue mussel Mytilus galloprovincialis (Craft et al, 2010), 17% in the Antarctic bivalve Laternula elliptica (Clark et al, 2010;Meyer et al, 2009), 24% in the Manila clam Ruditapes philippinarum (Milan et al, 2011), 25% in the krill Euphausia superba (Clark et al, 2011), 28% in the Yesso scallop Pactinopecten yessoensis (Hou et al, 2011) and 39% in the sea cucumber Apostichopus japonicus (Du et al, 2012). This is almost certainly due to the genome sequencing and annotation of a close relative; the Pacific oyster, Crassostrea gigas (Zhang et al, 2012a).…”

“…Indeed whole genome or transcriptome sequencing has proved a very efficient and cost effective method for expanding the sequence database for bivalves and other non-model species (i.e. Clark et al, 2010;Craft et al, 2010;Hou et al, 2011;Joubert et al, 2010;Meyer et al, 2009), and so was applied here to the transcriptome of the mangrove oyster C. brasiliana. In the last few years, several oyster genomes have become available, including the Pacific oyster Crassostrea gigas (Zhang et al, 2012a) and Pearl oyster Pinctada fucata (Takeuchi et al, 2012), significantly enriching the genomic resources for this animal model.…”

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

“…Therefore, according to KEGG pathway mapping, gene functions with the emphasis on biochemical pathways can be categorized (Hou et al, 2011 (Table S1). …”