, Volume 33, Issue 4, pp 930-943
Date: 10 Nov 2009

Discovering SNPs in Protein Coding Regions with StellaSNP: Illustrating the Characterization and Geographic Distribution of Polymorphisms in the Estuarine Anemone Nematostella vectensis

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Abstract

Single-nucleotide polymorphisms (SNPs) can be used to study the nucleotide diversity both within and between species. Furthermore, as some SNPs impact organismal phenotype, characterizing SNPs can provide insights into the relationship between genotype and phenotype and the adaptive evolution of populations. Model systems that combine a large quantity of available sequence data (e.g., large-scale expressed sequence tag (EST) sequencing projects) with diverse natural environments provide potent opportunities to investigate the evolution of adaptive nucleotide polymorphism in the wild. We developed a relational database of SNPs from 17,108 ESTs for the estuarine sea anemone Nematostella vectensis (www.stellabase.org/SNP). In these ESTs, we identified 20,063 candidate SNPs in 3,233 assembled contigs. Of these SNPs, 555 can be regarded with a high degree of confidence because the nucleotide variants occurring at that position were observed in at least two different ESTs. All 555 of these high-confidence SNPs were scored with respect to their location in coding or noncoding regions. Three hundred forty-three SNPs were within coding regions, 78 of which were nonsynonymous polymorphisms. We sequence-confirmed and analyzed the distribution of three nonsynonymous polymorphisms—one that occurs in the highly conserved homeodomain of the transcription factor tlx and two that occur in a deiodinase gene.

Adam M. Reitzel and James C. Sullivan contributed equally to this study.