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Updated: May 8, 2026
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A Converging Strategy for the Generation of a Virtually Sequenced cDNA Library from Unreferenced Pacific Oysters
Published on: June 13, 2019
Development of molecular resources for an intertidal clam, Sinonovacula constricta, using 454 transcriptome
Donghong Niu1, Lie Wang, Fanyue Sun
1Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China.
Plos One
|August 13, 2013
Summary
This study characterizes the razor clam transcriptome, identifying growth-related genes and valuable molecular markers like microsatellites (SSRs) and single nucleotide polymorphisms (SNPs). These findings advance genetic research for this commercially important bivalve species.
Area of Science:
- Marine Biology
- Genomics
- Aquaculture
Background:
- The razor clam (Sinonovacula constricta) is a commercially valuable intertidal bivalve.
- Limited genomic and transcriptomic data exist for S. constricta.
- Understanding its transcriptome is crucial for breeding and molecular marker development.
Purpose of the Study:
- To characterize the transcriptome of Sinonovacula constricta.
- To identify genes associated with growth traits.
- To discover molecular markers for genetic studies.
Main Methods:
- High-throughput deep sequencing using 454 pyrosequencing technology.
- Isolation of total RNA from various tissues (mantle, gill, liver, siphon, gonad, muscular foot).
- Bioinformatic analysis for read assembly, contig and singleton generation, and gene identification.
Main Results:
- Generated 859,313 high-quality reads, assembled into 16,323 contigs and 131,346 singletons.
- Identified 14,615 sequences with significant matches to known genes.
- Discovered 13,563 microsatellites (SSRs) and 13,634 single nucleotide polymorphism (SNP) loci, including novel growth-related genes.
Conclusions:
- De novo transcriptome sequencing provides a valuable resource for S. constricta.
- Identification of candidate growth factors and numerous SSRs/SNPs facilitates genetic studies.
- This research significantly impacts future genetic research and breeding programs for razor clams.
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