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Author ORCID Identifier
https://orcid.org/0009-0005-4426-0837
Date Available
5-8-2027
Year of Publication
2026
Document Type
Doctoral Dissertation
Degree Name
Doctor of Philosophy (PhD)
College
Agriculture, Food and Environment
Department/School/Program
Veterinary Science
Faculty
Theodore Kalbfleisch
Faculty
Emma Adam
Abstract
Long read sequencing and modern assembly algorithms have substantially advanced mammalian genome reconstruction yet repeat rich regions and complex structural variation remain difficult to resolve. This dissertation documents a progression in genome assembly strategies from reference refinement to haplotype-resolved and telomere-to-telomere (T2T) reconstruction. I first contributed to the development of the rat reference assembly GRCr8, integrating PacBio HiFi sequencing, Bionano optical mapping, and targeted curation. The resulting 2.85 Gb assembly achieved 98.7% chromosomal assignment, a scaffold N50 of 137 Mb, and a Merqury QV of 59.5. Next, haplotype-resolved T2T assemblies were generated for horse and donkey derived from a mule using trio-binning and long-read sequencing, improving BUSCO completeness and achieving phased chromosome-scale assemblies with a Merqury score of 52.5. Finally, integration of PacBio HiFi, ultra-long Oxford Nanopore reads, and Hi-C scaffolding enabled T2T reconstruction of the rat genome (SHRSP), achieving an overall QV of 65.0 and 15 of 22 chromosomes assembled gaplessly. Multiple high-quality rat assemblies further supported construction of a graph-based pangenome and systematic analysis of strain-specific structural variation. Together, these studies demonstrate stepwise gains in genome continuity, accuracy, and structural resolution enabled by long-read and haplotype-aware assembly strategies.
Digital Object Identifier (DOI)
https://doi.org/10.13023/etd.2026.249
Archival?
Archival
Funding Information
This study was supported by the National Institutes of Health Grant (no.: 1R01 HG011252-01A1 ) in 2023.
Recommended Citation
Li, Kai, "Technical Progression in Mammalian Genome Assembly: From Reference Refinement to Haplotype-Resolved Telomere-to-Telomere Reconstruction" (2026). Theses and Dissertations--Veterinary Science. 77.
https://uknowledge.uky.edu/gluck_etds/77
