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)

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.

进化生物学的一项经典研究目标，是鉴定与进化层面受关注的适应性性状相关的调控基因。近年来，下一代测序技术极大推动了对基因组资源匮乏物种的此类进化研究。更格卢鼠属（Dipodomys sp.）是适应性进化研究的典型类群：它们栖息于极端干旱的环境中，却凭借极高效率的肾脏功能与渗透调节（osmoregulation）能力，无需饮用淡水即可存活。
为鉴定更格卢鼠体内的水分保留相关基因，我们首先针对模式啮齿类——小家鼠（Mus musculus）与褐家鼠（Rattus norvegicus）开展了先验（a priori）生物信息学检索，以筛选出已知或疑似具备渗透调节功能的候选基因。随后，我们通过454焦磷酸测序（454 pyrosequencing）技术获得了446758条读段，以解析旗尾更格卢鼠（Dipodomys spectabilis）肾脏组织中的表达基因特征。此外，我们还通过筛选肾脏组织中高表达的基因，开展了后验（a posteriori）候选基因鉴定。
对更格卢鼠序列的分析结果显示，我们从小家鼠与褐家鼠检索得到的先验候选基因中，有9个在更格卢鼠体内存在同源序列；同时还鉴定出32个在肾脏中高表达的后验候选基因。上述候选基因中有两个——Slc12a1与Slc12a3——发生突变时会引发人类肾脏疾病，导致尿液浓缩功能障碍。这两个基因极有可能是荒漠啮齿类生理性水分保留的关键调控因子。