Development of molecular resources for an intertidal clam, Sinonovacula constricta, using 454 transcriptome sequencing.
BACKGROUND
The razor clam Sinonovacula constricta is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait.


RESULTS
Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated.


CONCLUSIONS
De novo sequencing of the razor clam S. constricta transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of S. constricta.
Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China.
Donghong
D
Niu
Lie
L
Wang
Fanyue
F
Sun
Zhanjiang
Z
Liu
Jiale
J
Li
D000818:Animals; D049872:Bivalvia / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D020224:Expressed Sequence Tags; D005880:Gills / Q000737:chemistry / Q000254:growth & development / Q000378:metabolism; D006066:Gonads / Q000737:chemistry / Q000254:growth & development / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics* / Q000378:metabolism; D008099:Liver / Q000737:chemistry / Q000254:growth & development / Q000378:metabolism; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D009132:Muscles / Q000737:chemistry / Q000378:metabolism; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D059467:Transcriptome
D036341:Intercellular Signaling Peptides and Proteins