DOI: 10.5061/dryad.ts98d
title: Data from: Natural selection and the genetic basis of osmoregulation in Heteromyid rodents as revealed by RNA-seq

description: One adaptation of ecological and evolutionary interest is the
 extraordinary ability of desert rodents to retain water during waste
 production. Much is known regarding the unique kidney physiology of
 kangaroo rats (Dipodomys spp.) and their ability to retain water during
 waste production, yet the genetic basis of these physiological adaptations
 is relatively unknown. Herein, we utilized RNA-seq data to conduct a
 comparative study to identify osmoregulatory genes expressed in Heteromyid
 rodents. We sequenced kidney tissue from two temperate desert species
 (Dipodomys spectabilis and Chaetodipus baileyi) from two separate
 subfamilies of the Heteromyidae and compared these transcriptomes to a
 tropical mesic species (Heteromys desmarestianus) from a third subfamily.
 The evolutionary history of these subfamilies provided a robust
 phylogenetic control that allowed us to separate shared evolutionary
 history from convergence. Using two methods to detect differential
 expression (DE), we identified 1,890 genes that showed consistent patterns
 of DE between the arid and mesic species. A three-species reciprocal BLAST
 analysis revealed 3,511 sets of putative orthologues that, upon comparison
 to known Mus musculus sequences, revealed 323 annotated and full length
 genic regions. Selection tests displayed evidence of positive selection
 (dn/ds &gt;1) on 6 genes in the two desert species and remained
 significant for one of these genes after correction for multiple testing.
 Thus, our data suggest that both the coding sequence and expression of
 genes have been shaped by natural selection to provide the genetic
 architecture for efficient osmoregulation in desert-adapted Heteromyid
 rodents.
description: Blast Descriptions for
 contigs from Dipodomys spectabilis kidney transcriptome
 assemblyThese are the
 preliminary blast descriptions for contigs from the combined assembly of
 454 and Illumina reads pooled from 4 individual Dipodomys spectabilis
 kidney libraries. Descriptions are from a BLASTx search of the Swiss-Prot
 database at e&lt;1x10^-6. The combined assembly was conducted in
 gsAssembler version 2.6 and contigs that were smaller than 100 bp have
 been removed. This accounts for the gaps in contig names (e.g. contig 2
 from the gsAssembler asembly was 35 bp long and removed prior to blast
 annotation so the first two contigs are contig 1 and contig
 3).D_spectabilis_blastdatafinalall.txtBlast Descriptions for contigs from Heteromys desmarestianus kidney transcriptome assemblyThese are the preliminary blast descriptions for contigs from the combined assembly of 454 and Illumina reads pooled from 4 individual Heteromys desmarestianus kidney libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e&lt;1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. contig 2 from the gsAssembler asembly was 25 bp long and removed prior to blast annotation so the first two contigs are contig 1 and contig 3).H_desm_kidney_blast_descriptions.txtD_spectabilis_kidney_transcriptomeCombined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.Blast Descriptions for contigs from Chaetodipus baileyi kidney transcriptome assemblyThese are the preliminary blast descriptions for contigs from the combined assembly of Illumina reads pooled from 4 individual Chaetodipus baileyi kidney libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e&lt;1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. contig 2 from the gsAssembler asembly was 25 bp long and removed prior to blast annotation so the first two contigs are contig 1 and contig 3).C_bail_blast_descriptions.txtC_baileyi_kidney_transcriptomeTranscriptome assembly from combined assembly Illumina reads. These reads were assembled first in Trinity and then fragmented and assembled in gsAssembler (see methods of manuscript for more details and rationale)H_desmarestianus_transcriptomeCombined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.Guide Tree for PAML analysisThis is the tree that was used in codeml as a guide tree for the branch and branch-site tests (see text of methods). The tree is unrooted to as is required for these tests. The two desert lineages, Dipodomys spectabilis and Chaetodipus baileyi have been marked with #1 to indicate them as foreground branches to be assigned a different rate than the rest of the tree. D_spec = Dipodomys spectabilis, C_bail = Chaetodipus baileyi, H_desm = Heteromys desmarestianus, M_musc = Mus musculus.COI_tree_unrooted_marked.newick