Chromosome level genome assemblies of Drosophila pseudoobscura determine Cuernavaca sequence inversion breakpoints and rearrangement mechanisms
Open Access
- Author:
- Dutzman, Nicole
- Area of Honors:
- Biology
- Degree:
- Bachelor of Science
- Document Type:
- Thesis
- Thesis Supervisors:
- Stephen Wade Schaeffer, Thesis Supervisor
Benoit A Dayrat, Thesis Honors Advisor - Keywords:
- Genetics
Drosophila pseudoobscura
Genome Assembly
Oxford Nanopore Sequencing
Chromosomal Inversions
Inversion Breakpoints
Cuernavaca
Heterozygosity
Repetitive Sequences - Abstract:
- Chromosomal inversions are a type of genomic structural variant that reorganizes gene order within and between species to create new gene arrangements. They have been demonstrated to play a role in generating mutant phenotypes, in adaptation to local environments, and in facilitating the speciation process. A rich gene arrangement polymorphism generated by overlapping inversions on the third chromosome of Drosophila pseudoobscura was discovered through studies conducted in the 1930s. The goal of these studies was to understand the genetic mechanisms that generate, establish, and maintain this polymorphism in the populations where they occur in the Southwestern United States. Gene arrangement frequencies vary among geographic localities with frequency shifts occurring with changes in environments. These frequency differences occur despite extensive gene flow, which is expected to prevent genetic differentiation. The focus of this thesis is to determine the mutational mechanisms that lead to rearrangement. As a case study, we focus on D. pseudoobscura strains containing the Cuernavaca (CU) chromosomal arrangement. We used the Oxford Nanopore long-read sequencing platform to determine the genome sequence of a D. pseudoobscura strain homozygous for the CU chromosome. We discovered that the original strain used in the sequencing was heterozygous for chromosomal arrangements, which provided an opportunity to determine the effect that strain heterozygosity has on the genome assembly process. Two D. pseudoobscura strains, one homozygous for the CU chromosomal arrangement and one heterozygous for the CU and Chiricahua (CH) chromosomal arrangements, were sequenced with Oxford Nanopore long-read sequencing technology. In the homozygous CU assembly, CU-specific breakpoints were found to be in areas containing repetitive sequences, suggesting that areas containing repeat content are prone to breakage to form chromosomal inversions. Comparisons between the homozygous CU and the heterozygous CU/CH assemblies showed that heterozygosity promoted fragmentation within genome assemblies, but otherwise, had no effect on assembly quality.