Understanding osmoregulation and immunity in heteromyid rodents through insights gained from RNA-Seq

Nicholas John Marra, Purdue University

Abstract

Species from the Heteromyidae form an exemplary system for studying the genetics of adaptation in a comparative framework. This new world family of rodents is comprised of three subfamilies (the Dipodomyinae, Perognathinae, and Heteromyinae) that range from the temperate/arid habitat of the southwestern United States down through Mexico and the mesic habitat of Central America into northern South America. In this dissertation I utilize 2nd generation sequencing technologies to characterize the genes expressed in biologically interesting tissues of three Heteromyid species. In sequencing the kidney and spleen transcriptomes of adult Dipodomys spectabilis (banner-tailed kangaroo rat), Chaetodipus baileyi (Bailey's pocket mouse), and Heteromys desmarestianus (forest spiny pocket mouse), I have sampled a representative of the Dipodomyinae, Perognathinae, and Heteromyinae, respectively. In chapter 1, I took a first pass at characterizing the kidney transcriptome of D. spectabilis. I identified a priori candidate genes important to kidney function from genetic model rodent species in an effort to identify potential drivers of D. spectabilis' recorded ability to retain water during the production of highly concentrated waste. I hypothesized that those candidates identified in D. spectabilis coupled with genes upregulated in this adapted organ would contain signatures of selection and have drastically divergent patterns of expression as hallmarks of their role in adaptation to a desert lifestyle. In chapter 2, I sought to identify if these or other genes exhibited clear patterns of differential expression and differentiation from the mesic H. desmarestianus that were driven by the different selective regimes on desert and mesic species. I also compared both species to C. baileyi , hypothesizing that any consistent differences seen in both C. baileyi and D. spectabilis relative to H. desmarestianus would be attributable to adaptation to arid habitat. In this chapter I identified a large number of genes in each species (roughly 11,000 per species) and filtered this set down to a subset of genes that either due to expression patterns or positive selection have evidence to be possible drivers of efficient osmoregulation in desert Heteromyids. For chapter 3, I focused on the genes expressed in spleen as an important tissue for immune response. Again I utilized the comparative framework of the Heteromyid family history in comparing the tropical H. desmarestianus to the temperate D. spectabilis and C. baileyi. My hypothesis was that greater selective pressure on immune response from increased pathogen diversity and burden in the tropics would fashion sequence evolution and different levels of gene regulation for immunity genes in H. desmarestianus. As in chapter 2, I generated a large amount of sequence data while winnowing down to a small number of solid candidate genes displaying positive selection and differential gene expression between the tropical and temperate Heteromyids. Due to the consistent patterns seen in the comparisons of D. spectabilis and C. baileyi against H. desmarestianus I predict that a subset of the genes identified here from kidney and spleen RNA-seq will prove to play a significant adaptive role in other vertebrates. Namely, the genes identified in chapters 1 and 2 will play roles in adaptation to water scarcity and those identified in chapter 3 will be consistently affected by the immune challenge of increased pathogen exposure in tropical species. (Abstract shortened by UMI.)

Degree

Ph.D.

Advisors

DeWoody, Purdue University.

Subject Area

Genetics

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