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6 results for “Ambystoma tigrinum”
Data from: Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex
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Data from: Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing
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Data from: Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)
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.
Data from: The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum)
BACKGROUND: Next-generation sequencing methods have contributed to rapid progress in the fields of genomics and population genetics. Using this high-throughput and cost-effective technology, a number of studies have estimated single nucleotide polymorphism (SNP) frequency by calculating the mean number of SNPs per unit sequence length (e.g., mean SNPs/kb). However, both read length and contig depth are highly variable and thus raise doubt about simple methods of SNP frequency estimation. RESULTS: We used 454 pyrosequencing to identify 2,980 putative SNPs in the eastern tiger salamander (Ambystoma tigrinum tigrinum) transcriptome, then constructed analytical models to estimate SNP frequency. The model which considered only contig length (i.e., the method employed in most published papers) was evaluated with very poor likelihood. Our most robust model considered read depth as well as contig length, and was 7.5 × 1055 times more likely than the length-only model. Using this novel modeling approach, we estimated SNP frequency in protein-coding (mRNA) and non-coding transcripts (e.g., small RNAs). We found little difference in SNP frequency in the contigs, but we found a trend of a higher frequency of SNPs in long contigs representing non-coding transcripts relative to protein-coding transcripts. These results support the hypothesis that long non-coding transcripts are less conserved than long protein-coding transcripts. CONCLUSIONS: A modeling approach (i.e., using multiple model construction and model selection approaches) can be a powerful tool for identifying selection on specific functional sequence groups by comparing the frequency and distribution of polymorphisms.
Data from: Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)
Open the record for dataset details and reuse information.
Data from: The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum)
Open the record for dataset details and reuse information.
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