Data from: Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)
| Main Authors: | Doyle, Jacqueline M., Siegmund, Gregor, Ruhl, Joseph D., Eo, Soo Hyung, Hale, Matthew C., Marra, Nicholas J., Waser, Peter M., DeWoody, J. Andrew |
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| Format: | info dataset Journal |
| Terbitan: |
, 2014
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4985741 |
Daftar Isi:
- 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.
- 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