Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

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.