Characterization of expressed sequence tag-derived single-nucleotide polymorphisms in the bay scallop Argopecten irradians irradians

Abstract

We describe herein the discovery of 3905 putative single-nucleotide polymorphisms (SNPs) from the alignment of 4968 sequences in a bay scallop Argopecten irradians irradians expressed sequenced tag (EST) database. The observed frequency of SNPs was estimated at one every 118.2 bp of contig sequences. Thirty of the SNPs were chosen for validation by tetra-primer amplification refractory mutation system-polymerase chain reaction procedure, and 17 of them were polymorphic with minor allele frequency ranging from 0.016 to 0.484. BLASTX gave significant hits for all but one of the 17 genotyped SNP-containing contigs, 11 of which were located in coding regions and all resulted in a synonymous substitution. Parentage simulation demonstrated that SNP markers were more sensitive to the number of parents compared with microsatellites, thus more SNPs were needed to counteract low polymorphism. A table of optimal codons was deduced from the analysis of the A. i. irradians EST dataset to explain the frequency difference for a specific SNP. It seems that the selection of codon usage may be partly responsible for the frequency difference between the two alleles of the coding SNPs. These are the first SNPs developed for the bay scallop and will provide a useful complement to currently available genetic markers.

A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction

“…This was indeed the most logical explanation for the extreme diversity observed in Ciona sea squirts (Small et al 2007; Tsagkogeorga et al 2012), another genus of ocean-dwelling broadcast spawners. As a high density of SNPs has been observed in the first marine bivalves studied (Sauvage et al 2007; Li et al 2009; Zhang and Guo 2010; Kim et al 2011), the same explanation was proposed (Sauvage et al 2007), but perhaps too hastily.…”

Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors

“…The rationale is that the pattern of choices between synonymous codons varies from one gene to another according to the type of genome in which the gene occurs (Grantham et al 1981). Knowledge of codon usage also could yield a wide range of information about an open reading frame, that is whether an open reading frame is likely to be a gene (Garnier-Gere and Dillmann 1992), and could provide useful information about the level of constraint on a gene in the genome (Li et al 2009). …”

Characterization of single nucleotide polymorphisms from expressed sequence tags of Chinese mitten crab Eriocheir sinensis

“…EST analysis is not only the most efficient approach for gene discovery, but it is also an effective approach for the development of DNA markers (Li et al 2009(Li et al , 2010a. In the present study, we detected a total of 3191 putative SNPs in the Eriocheir sinensis EST database, and the average SNP frequency was estimated at 128.4 bp of contig sequences.…”

“…Generally, locus discovery and genotyping are involved in the development of SNP markers. The rapidly developing expressed sequence tag (EST) databases make it possible to identify functionallyassociated SNPs (Li et al 2009), which are especially useful in correlative analysis and marker-assisted breeding. More recently, several highly multiplexed and ultra-high-throughout SNP genotyping systems have become available (Kwok 2001, Matsuzaki et al 2004.…”