Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations
Harris, Stephen E.; O'Neill, Rachel J.; Munshi-South, Jason (2014), Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations, Dryad, Dataset, https://doi.org/10.5061/dryad.6hc0f
Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of non-model species. We utilized two Next Generation Sequencing (NGS) platforms, 454 and SOLiD 5500XL, to assemble low coverage transcriptomes of the white-footed mouse (Peromyscus leucopus), a widespread and abundant native rodent in eastern North America. We sequenced liver mRNA transcripts from multiple individuals collected from urban populations in New York City and rural populations in undisturbed protected areas nearby and assembled a reference transcriptome using 1,080,065,954 SOLiD 5500XL (75 bp) reads and 3,052,640 454 GS FLX + reads. The reference contained 40,908 contigs with a N50 = 1,044 bp and a total content of 30.06 Megabases (Mb). Contigs were annotated from comparisons to Mus musculus (39.96% annotated) Uniprot databases. We identified 104,655 high quality single nucleotide polymorphisms (SNPs) and 65 single sequence repeats (SSRs) with flanking primers. We also used normalized read counts to identify putative gene expression differences in 15 genes between populations. There were 24 contigs significantly differentially expressed in urban populations compared to rural populations, with gene function annotations generally related to the translation and modification of proteins and those involved in immune responses. The individual transcriptomes generated in this study will be used to investigate evolutionary responses to urbanization. The reference transcriptome provides a valuable resource for the scientific community using North American Peromyscus species as emerging model systems for ecological genetics and adaptation.
New York Metropolitan Area