DOI: 10.5061/dryad.49s43
title: Data from: Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)

description: Historically, many population genetics studies have utilized
 microsatellite markers sampled at random from the genome and presumed to
 be selectively neutral. Recent studies, however, have shown that
 microsatellites can occur in transcribed regions, where they are more
 likely to be under selection. In this study, we mined microsatellites from
 transcriptomes generated by 454-pyrosequencing for three vertebrate
 species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma
 tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the
 occurrence of microsatellites across species; (ii) whether particular gene
 ontology terms were over-represented in genes that contained
 microsatellites; (iii) whether repeat motifs were located in untranslated
 regions or coding sequences of genes; and (iv) in silico polymorphism.
 Microsatellites were less common in tiger salamanders than in either lake
 sturgeon or kangaroo rats. Across libraries, trinucleotides were found
 more frequently than any other motif type, presumably because they do not
 cause frameshift mutations. By evaluating variation across reads assembled
 to a given contig, we were able to identify repeat motifs likely to be
 polymorphic. Our study represents one of the first comparative data sets
 on the distribution of vertebrate microsatellites within expressed genes.
 Our results reinforce the idea that microsatellites do not always occur in
 noncoding DNA, but commonly occur in expressed genes.
description: Ambystoma tigrinum gill
 transcriptome contigsWe extracted RNA from
 the gills of three A. tigrinum individuals. cDNA libraries were sequenced
 on a 454 Genome Sequencer. Sequences from all gill libraries were pooled
 and assembled into contigs using PCAP.salgill.txtAmbystoma tigrinum lung transcriptome contigsWe extracted RNA from the lungs of six A. tigrinum individuals. cDNA libraries were sequenced on a 454 Genome Sequencer. Sequences from all lung libraries were pooled and assembled into contigs using PCAP.sallung.fastaAmbystoma tigrinum skin transcriptome contigsWe extracted RNA from the skin of three A. tigrinum individuals. cDNA libraries were sequenced on a 454 Genome Sequencer. Sequences from all skin libraries were pooled and assembled into contigs using PCAP.salskin.txtAmbystoma tigrinum spleen transcriptome contigsWe extracted RNA from the spleens of six A. tigrinum individuals. cDNA libraries were sequenced on a 454 Genome Sequencer. Sequences from all spleen libraries were pooled and assembled into contigs using PCAP.salspleen.txtDipodomys spectabilis kidney transcriptome contigsWe extracted RNA from the kidneys of 4 individuals. Kidney cDNA libraries was sequenced on a 454 Genome Sequencer. 454 sequence reads from all kidney samples were pooled and assembled into contigs using PCAP.KRATKidney.contigs.bases.fastaDipodomys spectabilis spleen transcriptome contigsWe extracted RNA from the spleens of 4 individuals. Spleen cDNA libraries were sequenced on a 454 Genome Sequencer. 454 sequence reads from all kidney samples were pooled and assembled into contigs using PCAP.KRATSpleen.contigs.bases.fastaAcipenser fulvescens ovary transcriptome contigsWe extracted RNA from the ovary of a single individual. The cDNA library was sequenced on a 454 Genome Sequencer and reads were assembled into contigs using PCAP.female_contigs.fastaAcipenser fulvescens testes transcriptome contigsWe extracted RNA from the testes of a single individual. The cDNA library was sequenced on a 454 Genome Sequencer and reads were assembled into contigs using PCAP.male_contigs.fastaAssembly summary statisticsassembly summary statistics.xlsxContig msatcommander outputcontig msatcommander output.xlsxMicrosatellite variabilitymicrosatellite variability.xlsxSingleton msatcommander outputsingleton msatcommander output.xlsx