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.
annotated reproductive transcriptome
Annotated male Peromyscus eremicus reproductive tissue transcriptome (assembled from testes, epididymis, and vas deferens reads).
reproductive.annotated.fasta
42SeqsM2aPosSel
BLASTn results for 42 orthogroups under positive selection in P. eremicus (selection results were generated by PAML M2a analysis).
PAMLresults
Adjusted 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 orthogroups
The statistically significant p-values for the 42 orthogroups under positive selection in P. eremicus (selection results were generated by PAML M2a analysis)
significant_orthogroups.txt
transdecoder.gff3
Transdecoder .gff3 format output file for predicted protein coding regions for annotated transcriptome.
transdecoder.pep
Transdecoder .pep format output file for predicted protein coding regions for annotated transcriptome.
transdecoder.cds
Transdecoder .cds format output file for predicted protein coding regions for annotated transcriptome.
transdecoder.bed
Transdecoder .bed format output file for predicted protein coding regions for annotated transcriptome.
transdecoder.mRNA
Transdecoder .mRNA format output file for predicted protein coding regions for annotated transcriptome.
reproductive pfam
Pfam database matches annotation file for transcriptome (generated by dammit).
reproductive.pfam.gff3
reproductive rfam
Rfam database matches annotation file for transcriptome (generated by dammit).
reproductive.rfam.gff3
reproductive dammit
Complete annotation file for transcriptome, which includes annotations from all five searched databases generated by dammit.
reproductive.dammit.gff3
reproductive uniref
UniRef90 database matches annotation file for transcriptome (generated by dammit).
reproductive.uniref.gff3
epi.tpm.plus.ncRNA
Epididymis matches to the ncRNA Database.
vas.tpm.plus.ncRNA
Vas deferens matches to the ncRNA Database.
testes.tpm.plus.ncRNA
Testes matches to the ncRNA Database.
epi.tpm.plus.tcdb
Epididymis matches to the Transporter Classification Database.
testes.tpm.plus.tcdb
Testes matches to the Transporter Classification Database.
vas.tpm.plus.tcdb
Vas deferens matches to the Transporter Classification Database.
kallisto epi
Kallisto generated counts of expression for epididymis reads mapped to the annotated reproductive transcriptome.
kallisto.epi.tsv
kallisto testes
Kallisto generated counts of expression for testes reads mapped to the annotated reproductive transcriptome.
kallisto.testes.tsv
kallisto vas
Kallisto generated counts of expression for vas deferens reads mapped to the annotated reproductive transcriptome.
kallisto.vas.tsv