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Identifying Ateles geoffroyi Individuals Noninvasively using Third-Generation Sequencing Technologies

Bliss-Schryer, Michael Alexander
http://rave.ohiolink.edu/etdc/view?acc_num=kent1713991676334941

Abstract Details

2024, MA, Kent State University, College of Arts and Sciences / Department of Anthropology.
Genotyping animals is necessary for various field-based applications that require precise knowledge of the sampled individuals. Though feces are considered a low-quality source of host DNA, molecular techniques are increasingly prioritizing its usage for field-based noninvasive projects. Here, we describe a reproducible workflow to genotype individuals using a whole-genome sequencing approach with the portable, high throughput MinION MK1B and the BWA-GATK variant calling pipeline. After filtering, only 4 of the original 5,394 SNPs passed the filtering criteria, leading to an unsuccessful attempt to generate an informative multiloci SNP panel to confidently and accurately differentiate animals. In the filtered SNPs, 5 samples were entirely void of genotyping data. The majority of SNPs exhibited allelic dropout and a lack of called heterozygote genotypes, leading to the presumable false genotypes of the sampled individuals. On average, approximately 97% of the genome remained unsequenced, with only about one read covering each base in the mapped regions. Despite the limitations of employing a whole-genome sequencing approach to differentiate individuals with the MinION using feces, for species lacking known variants, this strategy may be an effective way to initially identify SNPs for subsequent resequencing and genotyping. Future studies are necessary to validate the authenticity of the identified SNPs and to assess their ability to discriminate individuals effectively with enrichment and targeted sequencing techniques.
Rafaela Takeshita (Advisor)
Sangeet Lamichhaney (Committee Member)
Richard Meindl (Committee Member)
Anthony Tosi (Committee Member)
92 p.
Bioinformatics; Genetics
Whole-Genome Sequencing, MinION, GATK, Noninvasive, Genotyping, SNPs

Recommended Citations

Citations

  • Bliss-Schryer, M. A. (2024). Identifying Ateles geoffroyi Individuals Noninvasively using Third-Generation Sequencing Technologies [Master's thesis, Kent State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=kent1713991676334941

    APA Style (7th edition)

  • Bliss-Schryer, Michael. Identifying Ateles geoffroyi Individuals Noninvasively using Third-Generation Sequencing Technologies. 2024. Kent State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=kent1713991676334941.

    MLA Style (8th edition)

  • Bliss-Schryer, Michael. "Identifying Ateles geoffroyi Individuals Noninvasively using Third-Generation Sequencing Technologies." Master's thesis, Kent State University, 2024. http://rave.ohiolink.edu/etdc/view?acc_num=kent1713991676334941

    Chicago Manual of Style (17th edition)

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© 2024, all rights reserved.
This open access ETD is published by Kent State University and OhioLINK.