ArticlePloS one2013
Transcriptome sequencing of Zhikong scallop (Chlamys farreri) and comparative transcriptomic analysis with Yesso scallop (Patinopecten yessoensis).
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 59 citations in OpenAlex.
- Transcriptome Analysis Reveals MAPK/AMPK as a Key Regulator of the Inflammatory Response in PST Detoxification inToxins · 2022Article
- De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development inLife (Basel, Switzerland) · 2021Article
- In silico determination of nitrogen metabolism in microbes from extreme conditions using metagenomics.Archives of microbiology · 2021Article
- Hyperaccumulation of cadmium by scallop Chlamys farreri revealed by comparative transcriptome analysis.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2020Article
- Histological and Expression Differences Among Different Mantle Regions of the Yesso Scallop (Patinopecten yessoensis) Provide Insights into the Molecular Mechanisms of Biomineralization and Pigmentation.Marine biotechnology (New York, N.Y.) · 2019Article
- Transcriptomic Analysis of Marine GastropodMarine drugs · 2019Article
- The transcriptomic responses of the ark shell, Anadara broughtonii, to sulfide and hypoxia exposure.Molecular biology reports · 2019Article
- Transcriptome analysis of air-breathing land slug, Incilaria fruhstorferi reveals functional insights into growth, immunity, and reproduction.BMC genomics · 2019Article
- HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay.Genome research · 2018Article
- Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins.Nature communications · 2017Article
- Article
- Transcriptomics Analysis of Crassostrea hongkongensis for the Discovery of Reproduction-Related Genes.PloS one · 2015Article
- Mantle Branch-Specific RNA Sequences of Moon Scallop Amusium pleuronectes to Identify Shell Color-Associated Genes.PloS one · 2015Article
- Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes.BMC genomics · 2014Article
- High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Large-scale development of gene-associated single-nucleotide polymorphism markers for molluscan population genomic, comparative genomic, and genome-wide association studies.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Article
- Gene discovery through transcriptome sequencing for the invasive mussel Limnoperna fortunei.PloS one · 2014Article
- A scallop IGF binding protein gene: molecular characterization and association of variants with growth traits.PloS one · 2014Article
- Identification of reference genes for qRT-PCR analysis in Yesso scallop Patinopecten yessoensis.PloS one · 2013Article
Corrections and comments
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBivalves play an important role in the ecosystems they inhabit and represent an important food source all over the world. So far limited genetic research has focused on this group of animals largely due to the lack of sufficient genetic or genomic resources. Here, we performed de novo transcriptome sequencing to produce the most comprehensive expressed sequence tag resource for Zhikong scallop (Chlamys farreri), and conducted the first transcriptome comparison for scallops.
resultsIn a single 454 sequencing run, 1,033,636 reads were produced and then assembled into 26,165 contigs. These contigs were then clustered into 24,437 isotigs and further grouped into 20,056 isogroups. About 47% of the isogroups showed significant matches to known proteins based on sequence similarity. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified through Gene ontology (GO) and KEGG pathway analyses. Transcriptome comparison with Yesso scallop (Patinopecten yessoensis) revealed similar patterns of GO representation. Moreover, 38 putative fast-evolving genes were identified through analyzing the orthologous gene pairs between the two scallop species. More than 46,000 single nucleotide polymorphisms (SNPs) and 350 simple sequence repeats (SSRs) were also detected.
conclusionOur study provides the most comprehensive transcriptomic resource currently available for C. farreri. Based on this resource, we performed the first large-scale transcriptome comparison between the two scallop species, C. farreri and P. yessoensis, and identified a number of putative fast-evolving genes, which may play an important role in scallop speciation and/or local adaptation. A large set of single nucleotide polymorphisms and simple sequence repeats were identified, which are ready for downstream marker development. This transcriptomic resource should lay an important foundation for future genetic or genomic studies on C. farreri.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.