DOI: 10.5061/dryad.01c3t
title: Data from: Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)

description: Rodents of the genus Peromyscus have become increasingly utilized models
 for investigations into adaptive biology. This genus is particularly
 powerful for research linking genetics with adaptive physiology or
 behaviors, and recent research has capitalized on the unique opportunities
 afforded by the ecological diversity of these rodents. Well characterized
 genomic and transcriptomic data is intrinsic to explorations of the
 genetic architecture responsible for ecological adaptations. Therefore,
 this study characterizes the transcriptome of three male reproductive
 tissues (testes, epididymis and vas deferens) of Peromyscus eremicus
 (Cactus mouse), a desert specialist. The transcriptome assembly process
 was optimized in order to produce a high quality and substantially
 complete annotated transcriptome. This composite transcriptome was
 generated to characterize the expressed transcripts in the male
 reproductive tract of P. eremicus, which will serve as a crucial resource
 for future research investigating our hypothesis that the male Cactus
 mouse possesses an adaptive reproductive phenotype to mitigate water-loss
 from ejaculate. This study reports genes under positive selection in the
 male Cactus mouse reproductive transcriptome relative to transcriptomes
 from Peromyscus maniculatus (deer mouse) and Mus musculus. Thus, this
 study expands upon existing genetic research in this species, and we
 provide a high quality transcriptome to enable further explorations of our
 proposed hypothesis for male Cactus mouse reproductive adaptations to
 minimize seminal fluid loss.
description: annotated reproductive
 transcriptomeAnnotated male
 Peromyscus eremicus reproductive tissue transcriptome (assembled from
 testes, epididymis, and vas deferens reads).reproductive.annotated.fasta42SeqsM2aPosSelBLASTn results for 42 orthogroups under positive selection in P. eremicus (selection results were generated by PAML M2a analysis).PAMLresultsAdjusted p-values for all orthogroup comparisons using null vs. alternative model evaluations with P. eremicus in as the foreground lineage (selection results were generated by PAML M2a analysis)significant orthogroupsThe statistically significant p-values for the 42 orthogroups under positive selection in P. eremicus (selection results were generated by PAML M2a analysis)significant_orthogroups.txttransdecoder.gff3Transdecoder .gff3 format output file for predicted protein coding regions for annotated transcriptome.transdecoder.pepTransdecoder .pep format output file for predicted protein coding regions for annotated transcriptome.transdecoder.cdsTransdecoder .cds format output file for predicted protein coding regions for annotated transcriptome.transdecoder.bedTransdecoder .bed format output file for predicted protein coding regions for annotated transcriptome.transdecoder.mRNATransdecoder .mRNA format output file for predicted protein coding regions for annotated transcriptome.reproductive pfamPfam database matches annotation file for transcriptome (generated by dammit).reproductive.pfam.gff3reproductive rfamRfam database matches annotation file for transcriptome (generated by dammit).reproductive.rfam.gff3reproductive dammitComplete annotation file for transcriptome, which includes annotations from all five searched databases generated by dammit.reproductive.dammit.gff3reproductive unirefUniRef90 database matches annotation file for transcriptome (generated by dammit).reproductive.uniref.gff3epi.tpm.plus.ncRNAEpididymis matches to the ncRNA Database.vas.tpm.plus.ncRNAVas deferens matches to the ncRNA Database.testes.tpm.plus.ncRNATestes matches to the ncRNA Database.epi.tpm.plus.tcdbEpididymis matches to the Transporter Classification Database.testes.tpm.plus.tcdbTestes matches to the Transporter Classification Database.vas.tpm.plus.tcdbVas deferens matches to the Transporter Classification Database.kallisto epiKallisto generated counts of expression for epididymis reads mapped to the annotated reproductive transcriptome.kallisto.epi.tsvkallisto testesKallisto generated counts of expression for testes reads mapped to the annotated reproductive transcriptome.kallisto.testes.tsvkallisto vasKallisto generated counts of expression for vas deferens reads mapped to the annotated reproductive transcriptome.kallisto.vas.tsv