Dissertation/Thesis Abstract

Comparative Mitogenomics of the Rodent Suborder Castorimorpha
by Greenia, Haley Shea, M.S., Tarleton State University, 2020, 59; 28024140
Abstract (Summary)

Although many mammalian mitogenomes have been sequenced, there are only three documented from the rodent suborder Castorimorpha. These three are from two beavers and a kangaroo rat. A genus of Castorimorpha, Geomys, represents 12 species of pocket gophers. In the last 20 years, three studies comprise documentation of mitochondrial DNA variation across Geomys through two mitochondrial genes. No complete mitogenome of pocket gophers has been published. This study sequenced Geomys species and carried out a comparative analysis across the suborder to the previously sequenced mitochondrial genomes of castorimorphs. The specific research objectives are to compare gene arrangement, tRNA secondary structures, gene content, codon usage, evolutionary patterns of protein coding genes, and to construct a phylogenetic tree. Extracted DNA was serially diluted to find the minimum concentration of mitochondrial DNA required to amplify while reducing contamination by nuclear insertions of mitochondrial DNA (numts). This dilution was amplified with Rolling Circle Amplification, tagmented with indices through Nextera XT DNA Library Prep Kit, and sequenced with Illumina technology. Assembly of mitogenomes will be conducted with NOVOPlasty. Annotation of mitogenomes were first identified with MITOS2 and confirmed through an alignment to other rodents. Evolutionary patterns of protein coding genes were measured by nonsynonymous to synonymous ratios, or Ka/Ks in Mega-X using the Nei-Gojobori method with Jukes-Cantor correction. tRNA structures will be predicted with MITOS2. Codon usage per 1000 codons will be calculated by Sequence Manipulation Suite. Maximum likelihood tree was constructed under Mega-X under the GTR model with gamma distribution with invariant sites. Of the 12 specimens sequenced, 8 specimens resulted in successful mitogenome assemblies. However, only one control region of the 8 was assembled. The gene arrangement and tRNA secondary structures are typical of other metazoans. There are unique features among the castorimorphs such as insertions exclusive to Dipodomys, start codons only used by Castor, and start and stop codons unique to G. breviceps. Codon usage was relatively similar among all castorimorphs. Castorimorphs indicated an evolutionary pattern among protein coding genes: strong negative selection for cox1-cox3 and cytb, and mildly negative selection for atp8, nad2, and nad6. A maximum likelihood tree of concatenated PCGs supports the evolutionary relationships among Castor, Dipodomys, and Geomys documented by previous workers, but with stronger support at a bootstrap value of 100% at each node.

Indexing (document details)
Advisor: Pfau, Russell
Commitee: Edwards, Dustin, Herrmann, Kristin
School: Tarleton State University
Department: Department of Biological Sciences
School Location: United States -- Texas
Source: MAI 82/2(E), Masters Abstracts International
Subjects: Biology, Genetics, Molecular biology
Keywords: Castorimorph, Comparative mitochondrial DNA, Complete mitochondrial DNA, Geomys, Mitogenomic
Publication Number: 28024140
ISBN: 9798664729610
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