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Gene Family Evolution of Digestive Enzymes in the American Pika: A Comparative Genomics Analysis

Raba, Teresa J
http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1715016537668171

Abstract Details

2024, BS, Kent State University, College of Arts and Sciences / Department of Biological Sciences.
The American pika (Ochotona princeps) is an herbivorous mammal that inhabits rocky, mountainous regions across the western United States. Although they share a common ancestor with rabbits and other species in the order Lagomorpha, American pikas have a specialized diet due to an inability to migrate from their narrow habitat range. Gene families are made up of genes similar in sequence and function among species that share a common ancestor. Increases in gene copy number due to random duplication results in gene family expansion, whereas gene deletion results in family contraction. Evolutionary divergence can result in functional and genetic differences in the way that pikas and other lagomorphs digest their food with the help of enzymes. We hypothesized that American pikas have undergone lineage-specific expansions or contractions in gene families encoding enzymes (particularly digestive enzymes), allowing the species to digest available food in their narrow and changing habitat. Using the computational tool, OrthoFinder, protein sequences of the American pika were compared to seven distantly related taxa to identify gene families. CAFE5 analysis identified copy number evolution compared to the most recent common ancestor of all eight species. Functional enrichment analysis with PANTHER showed gene families related to digestive enzymes are significantly expanded in the American pika compared to other species. This indicates that protease digestive enzymes are more highly expressed in the American pika, possibly contributing to their metabolism of plants that inhabit their habitat.
Sangeet Lamichhaney, PhD (Advisor)
Rafaela Takeshita, PhD (Committee Member)
Mark Kershner, PhD (Committee Member)
Helen Piontkivska, PhD (Committee Member)
42 p.
Bioinformatics; Biology
copy number evolution; gene duplication; computational biology; OrthoFinder

Recommended Citations

Citations

  • Raba, T. J. (2024). Gene Family Evolution of Digestive Enzymes in the American Pika: A Comparative Genomics Analysis [Undergraduate thesis, Kent State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1715016537668171

    APA Style (7th edition)

  • Raba, Teresa. Gene Family Evolution of Digestive Enzymes in the American Pika: A Comparative Genomics Analysis. 2024. Kent State University, Undergraduate thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1715016537668171.

    MLA Style (8th edition)

  • Raba, Teresa. "Gene Family Evolution of Digestive Enzymes in the American Pika: A Comparative Genomics Analysis." Undergraduate thesis, Kent State University, 2024. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1715016537668171

    Chicago Manual of Style (17th edition)

ksuhonors1715016537668171
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© 2024, all rights reserved.
This open access ETD is published by Kent State University Honors College and OhioLINK.
Release 3.2.12