The origin and evolution of inversion breakpoint sequences on the third chromosome of Drosophila pseudoobscura

Open Access
Randolph, Haley Elizabeth
Area of Honors:
Bachelor of Science
Document Type:
Thesis Supervisors:
  • Stephen Wade Schaeffer, Thesis Supervisor
  • James Harold Marden, Honors Advisor
  • chromosomal rearrangement
  • breakpoint sequence evolution
  • inversion mutation
  • paracentric inversion
  • Drosophila pseudoobscura
The chromosomal arrangements of Drosophila pseudoobscura provide an excellent model system to understand the mechanisms that generate novel chromosomal inversions. D. pseudoobscura has over thirty different chromosomal arrangements generated by a series of overlapping paracentric inversions on the third chromosome. Two major models of rearrangement are postulated: repeat-mediated events and staggered-cut single-stranded break events. Analyzing the DNA sequences at breakpoints of both the ancestral and derived arrangements of inversion mutations will likely reveal the apparent mechanism that led to the formation of the chromosomal arrangements. To study the mechanisms of rearrangement, we looked at three different inversion mutations in D. pseudoobscura. The locations of the breakpoint sequences were determined from three kilobase large-insert mate-pair libraries whose reads were generated on an Illumina HiSeq 2000 sequencing platform. Sequences were assembled from short-insert paired-end libraries, and a gene flanking the breakpoint served as a starting point for sequence assembly. We have determined the ancestral and derived breakpoint sequences of the Standard to Pikes Peak mutation, the derived breakpoint sequences of the Santa Cruz to Tree Line mutation, and the ancestral breakpoint sequences of the Standard to Arrowhead mutation. Bioinformatics investigation suggests that short, common repeat sequences of about 100 base pairs comprise a main portion of the breakpoint regions. These repeat sequences are enriched within all breakpoint sequences analyzed, suggesting that these shared repeats play a general role in the inversion mutational process. No evidence for boundary gene duplication or transposable element involvement exists in the breakpoint sequences, supporting the repeat-mediated model of chromosomal arrangement formation.