Data from: A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat)
Marra, Nicholas J., Purdue University
Eo, Soo Hyung, Purdue University
Hale, Matthew C., Purdue University
Waser, Peter M., Purdue University
DeWoody, J. Andrew, Purdue University
Published Mar 17, 2015 on Dryad.
Cite this dataset
Marra, Nicholas J. et al. (2015). Data from: A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat) [Dataset]. Dryad. https://doi.org/10.5061/dryad.sf654
One common goal in evolutionary biology is the identification of genes underlying adaptive traits of evolutionary interest. Recently next-generation sequencing techniques have greatly facilitated such evolutionary studies in species otherwise depauperate of genomic resources. Kangaroo rats (Dipodomys sp.) serve as exemplars of adaptation in that they inhabit extremely arid environments, yet require no drinking water because of ultra-efficient kidney function and osmoregulation. As a basis for identifying water conservation genes in kangaroo rats, we conducted a priori bioinformatics searches in model rodents (Mus musculus and Rattus norvegicus) to identify candidate genes with known or suspected osmoregulatory function. We then obtained 446,758 reads via 454 pyrosequencing to characterize genes expressed in the kidney of banner-tailed kangaroo rats (Dipodomys spectabilis). We also determined candidates a posteriori by identifying genes that were overexpressed in the kidney. The kangaroo rat sequences revealed nine different a priori candidate genes predicted from our Mus and Rattus searches, as well as 32 a posteriori candidate genes that were overexpressed in kidney. Mutations in two of these genes, Slc12a1 and Slc12a3, cause human renal diseases that result in the inability to concentrate urine. These genes are likely key determinants of physiological water conservation in desert rodents.
These are the trimmed fasta and qual files for each of the individual kidney libraries and all of the individual libraries together in a whole tissue file
Trimmed .fasta and .qual files for each individual spleen library and for the total tissue library
These are the .fasta and .ace files for all of the contigs from individual kidney assemblies as well as all of the kidney libraries assembled into one total 'kidney' assembly as described in the paper.
This file contains all of the spleen .fasta and .ace files for the contigs of all assemblies of individual spleen libraries as well as a total tissue 'spleen' library
Individual .sff files for each of four individuals, for kidney
Individual .sff files for each of four individuals, for spleen
Single .sff file with all reads from the four individual kidney libraries concatenated into one total tissue file
Single .sff file with all reads from the four individual spleen libraries concatenated into one total tissue file