Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome

Abstract

A total of 2,970 EST-SSRs (2.38%) were identified by transcriptome sequencing of clam Meretrix meretrix (751,970 reads, ~310.82 Mbp), using 454 Genome Sequencer FLX next-generation sequencing platform. Dinucleotide SSR was the dominant repeat type (40.2%), followed by trinucleotide (37.8%), tetranuleotide (12.0%) and pentanucleotide (2.0%) SSR. The dominant repeat motif was AT (71.3%) in the dinucleotide SSR type and AAC (45.6%) in the trinucleotide SSR type. Nearly 79% of all microsatellites had flanking sequences suitable for PCR primer design. Half of PAL were found to be polymorphic in a subset of 40 primer pairs randomly selected. Specifically, the density of dinucleotide, trinucleotide and tetranucleotide repeats showed significant variation among four development stages (trochophore, D-veliger, pediveliger and postlarva). The results suggested that dinucleotide, trinucleotide and tetranucleotide SSRs may play an important role in contributing to the different expression profiles in larval stages.

Development of Molecular Resources for an Intertidal Clam, Sinonovacula constricta, Using 454 Transcriptome Sequencing

“…The development of microsatellite markers is time-consuming and expensive, as it requires preparation of genomic libraries, hybridization to detect positive clones, plasmid isolation and sequencing [40]. Next-generation sequencing provides an efficient and cost-effective way to identify microsatellites [41].…”

Sequencing and Characterization of Striped Venus Transcriptome Expand Resources for Clam Fishery Genetics

“…The recent genome sequencing fulfilment of C. gigas has opened new chances towards the production of targeted gene knock down individuals [22], [23]. In addition, the forthcoming accomplishment of de novo sequencing and annotation of the two gastropods Aplysia califonica and Lottia gigantea complete genomes and the recently published Meretrix meretrix (Bivalvia, [24]), Laternula eliptica [Bivalvia, 16], Solemya velum and Nucula nitidosa (Bivalvia, [25]), Lymnaea stagnalis (Gasteropoda, [26]) and Crepidula fornicate (Gasteropoda, [27]) transcriptomes and EST resources will provide a precious instrument for the analysis of mollusc species sequences.…”

De novo assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster Pinctada maxima

“…The PCR success rate (68.3%) was comparative with the results obtained in other shellfish species. For example, success rates was 65.0% in the clam Meretrix meretrix, 15) 50.0% in the clam Mercenaria mercenaria, 38) and 80.7% in the oyster Crassostrea virginica.…”

“…Simple sequence repeat (SSR) markers are generally preferred over random amplification of polymorphic DNAs (RAPD) and amplified fragment length polymorphisms (AFLP) because of their many advantages, which include genetic codominance, abundance, dispersal throughout the genome, multi-allelic variation, high reproducibility, and high level of polymorphism. 14,15) SSRs can be divided into expressed sequence tag (EST)-SSRs and genomic SSRs on the basis of the original sequences used to identify simple repeats. EST-SSRs are derived from expressed sequences, which are more evolutionarily conserved than non-coding sequences; therefore, EST-SSR markers have a relatively higher transferability than genomic SSRs.…”