DOI: 10.5061/dryad.6hc0f
title: Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

description: 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.
description: Table S1. SSR sequences
 and primers (doc file)Table of microsatellite
 repeats identified using MsatCommander and sorted by motif. Only repeats
 with suitable flanking sequence for primer design were kept. Primer
 sequences designed using Primer3 are also listed.Table_S1_Peromyscus_SSR.docxTable S2. Chromosomal order and assignment (csv file)Comma-delimited spreadsheet listing contig names that were assigned to Peromyscus chromosomes. Contigs are sorted by start of alignment in the chromosome and are displayed in typical BLAST –m6 (tabular) format.TableS2_Peromyscus_Linkage_Map.xlsxContig sequences for P. leucopus transcriptome (fasta file)Transcriptome contigs assembled from raw SOLiD 5500 xl sequencing reads using Trinity. Only contigs with high-quality open reading frames identified from Transdecoder and unique contigs with best match hits to Mus musculus Uniprot protein database using BLASTN were kept.Pleucopus_Transcriptome_Contigs.fastaInformation on SNPs identified from transcriptome data (vcf file)SNPs identified from transcriptome alignment files in variant call format. SNPs were identified using GATK. Parameters and filters for calling SNPs are listed in header. Additional hard filters include removal of SNPs where every individual was heterozygous, overall SNP depth &gt; 10, overall SNP depth &lt; 350, and minor allele frequency (MAF) &gt; 0.025.Pleucopus_Filered_SNPs.vcfAnnotation information, BLAST results, Gene Ontology (.dat file for Blast2GO)Standard input file for BLAST2GO. This file can be loaded directly into .jnlp executable file downloaded from BLAST2GO website. Includes BLASTX results against NCBI’s non-redundant protein database and Gene Ontology information based on best hit gene matches.Pleucopus_Transcriptome_blast2go.datR scripts, bash scripts, and full analysis workflow (txt file)This text file represents the working lab notebook of all software, scripts, and command line usage dating from when the raw data were received to when the final figures and tables were produced.LabNotebook_Scripts.txtContig sequences for P. leucopus transcriptome (fasta file)A second transcriptome is included named, “Pleucopus_Transcriptome_Contigs_Annotated.fasta”. This file includes unique contigs that mapped to the Mus musculus transcriptome. Gene annotations are included in the header for each sequence.Pleucopus_Transcriptome_Contigs_Annotated.fastaAlternative splice events identified in Peromyscus leucopus transcriptomeThis FASTA file contains two sequences for each alternative splicing sequence, labeled as upper and lower splice, that was identified in the Peromyscus leucopus transcriptome.Pleucopus_Transcriptome_AlternativeSplice_Events.fastaContigs from Peromyscus leucopus transcriptome that represent splice variantsPleucopus_Transcriptome_AlternativeSplice_Contigs.fasta