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 >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.
Blast Descriptions for contigs from Dipodomys spectabilis kidney transcriptome assembly
These 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<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.txt
Blast Descriptions for contigs from Heteromys desmarestianus kidney transcriptome assembly
These 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<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.txt
D_spectabilis_kidney_transcriptome
Combined 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 assembly
These 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<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.txt
C_baileyi_kidney_transcriptome
Transcriptome 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_transcriptome
Combined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.
Guide Tree for PAML analysis
This 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