Nicole Dutzman Honors Thesis Appendix

Appendix Files for Nicole Dutzman Honors Thesis. These files reflect downstream processing of long read sequencing data for the Drosophila pseudoobscura strain CUSPE1234-1_B carrying the Cuernavaca gene arrangement on the third chromosome. The strain was collected in San Pablo Etla, Oaxaca, Mexico by Dr. Theresa Markow.

Thesis 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.

Citation

Schaeffer, Stephen; Dutzman, Nicole (2022). Nicole Dutzman Honors Thesis Appendix [Data set]. Scholarsphere.

Files

Metadata

Work Title Nicole Dutzman Honors Thesis Appendix
Access
Penn State
Creators
  1. Stephen Schaeffer
  2. Nicole Dutzman
Keyword
  1. Genetics
  2. Drosophila pseudoobscura
  3. Genome assembly
  4. Oxford Nanopore Sequencing
  5. Chromosomal inversions
  6. Inversion breakpoints
  7. Cuernavaca
  8. Heterozygosity
  9. Repetitive sequences
License In Copyright (Rights Reserved)
Work Type Dataset
Publication Date March 31, 2022
Related URLs
Deposited March 31, 2022

Versions

Analytics

Collections

This resource is currently not in any collection.

Work History

Version 1
published

  • Created
  • Updated
  • Added Creator Stephen Schaeffer
  • Added Creator Nicole Dutzman
  • Added Heterozygous CUCH Against Homozygous CU Blast.xlsx
  • Added Heterozygous CUCH Data.xlsx
  • Added Homozygous CU Data.xlsx
  • Added CU_SPE123_4-1_B_Flye_Assembly_info_v3.tabular
  • Added CU_SPE123_4-1_B_Heterozygous_Flye_Assembly_v3.tabular
  • Added CU_SPE123_4-1_B_Homozygous_Assembly_v1.tabular
  • Added CU_SPE123_4-1_B_Heterozygous_Flye_Assembly_v3_graphical_fragment_assembly].txt
  • Added CU_SPE123_4-1_B_Homozygous_Assembly_v1.txt
  • Added CU_SPE123_4-1_B_Heterozygous_Flye_Assembly_v3.fasta
  • Added CU_SPE123_4-1_B_Heterozygous_FlyeAssembly_v3.fasta
  • Added CU_SPE123_4-1_B_Homozygous_Assembly_v1.fasta
  • Added CU_SPE123_4-1_B_Heterozygous_Flye_Assembly_v3.graph_dot
  • Added CU_SPE123_4-1_B_Homozygous_Assembly_v1.graph_dot
  • Added Heterozygous Chromeister Metainfo.csv
  • Added Homozygous Chromeister Metainfo.csv
  • Added Additional Genome Assembly Calculations.xlsx
  • Updated Description, Publication Date, License Show Changes
    Description
    • Appendix Files for Nicole Dutzman Honors Thesis. These files reflect downstream processing of long read sequencing data for the Drosophila pseudoobscura strain CU_SPE123_4-1_B carrying the Cuernavaca gene arrangement on the third chromosome. The strain was collected in San Pablo Etla, Oaxaca, Mexico by Dr. Theresa Markow.
    Publication Date
    • 2022-03-31
    License
    • https://creativecommons.org/licenses/by/4.0/
  • Updated License Show Changes
    License
    • https://creativecommons.org/licenses/by/4.0/
    • https://rightsstatements.org/page/InC/1.0/
  • Published
  • Updated Keyword, Description, Related URLs Show Changes
    Keyword
    • Genetics, Drosophila pseudoobscura, Genome assembly, Oxford Nanopore Sequencing, Chromosomal inversions, Inversion breakpoints, Cuernavaca, Heterozygosity, Repetitive sequences
    Description
    • Appendix Files for Nicole Dutzman Honors Thesis. These files reflect downstream processing of long read sequencing data for the Drosophila pseudoobscura strain CU_SPE123_4-1_B carrying the Cuernavaca gene arrangement on the third chromosome. The strain was collected in San Pablo Etla, Oaxaca, Mexico by Dr. Theresa Markow.
    • Appendix Files for Nicole Dutzman Honors Thesis. These files reflect downstream processing of long read sequencing data for the Drosophila pseudoobscura strain CU_SPE123_4-1_B carrying the Cuernavaca gene arrangement on the third chromosome. The strain was collected in San Pablo Etla, Oaxaca, Mexico by Dr. Theresa Markow.
    • Thesis 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.
    Related URLs
    • https://honors.libraries.psu.edu/catalog/7878nld5180
  • Updated