title: 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.
authors.affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Quingdao, China.
authors.forename: Hongxia
authors.initials: H
authors.lastname: Wang
authors.forename: Pin
authors.initials: P
authors.lastname: Huan
authors.forename: Xia
authors.initials: X
authors.lastname: Lu
authors.forename: Baozhong
authors.initials: B
authors.lastname: Liu
mesh_terms: D000818:Animals; D001483:Base Sequence; D049872:Bivalvia / Q000235:genetics* / Q000378:metabolism; D017931:DNA Primers / Q000235:genetics; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D014644:Genetic Variation; D008018:Life Cycle Stages / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D017931:DNA Primers