University of Illinois Urbana-Champaign

Chromosomal assembly and comparative analysis of the red fox (Vulpes vulpes) genome

Rando, Halie M.

Content Files
RANDO-THESIS-2015.pdf

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https://hdl.handle.net/2142/88223

Description

Title
Chromosomal assembly and comparative analysis of the red fox (Vulpes vulpes) genome
Author(s)
Rando, Halie M.
Issue Date
2015-07-21
Director of Research (if dissertation) or Advisor (if thesis)
Kukekova, Anna V
Department of Study
Animal Sciences
Discipline
Bioinformatics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
M.S.
Degree Level
Thesis
Date of Ingest
2015-09-29T20:50:22Z
Keyword(s)
  • genome assembly
  • red fox
  • silver fox
  • chromosome
  • bioinformatics
  • genomics
  • 10K Genomes
Abstract
In the early days of genomics, the development of a reference genome was an expensive, collaborative undertaking reserved only for traditional and popular model organisms; however, in a theoretical shift highlighted most clearly by the goals of the Genome 10K Project, the advent of next-generation sequencing (NGS) technology has resulted in a shift of focus towards the development of reference genomes for a variety of species less commonly studied. One non-traditional model organism selected as a priority species for the Genome 10K Project is the red fox (Vulpes vulpes), and specifically a fox from an experimental breeding project in which silver foxes (a melanistic variant of the red fox) have been selected over the past several decades to exhibit extreme behavioral phenotypes. The population consists of a strain of hyper-aggressive foxes and a strain of hyper-docile foxes, offering a model system through which the genetic underpinnings of behavior, as well as the genetic correlates of domestication, can be investigated. The draft red fox genome, which was developed at BGI, has a sequence depth of 94x and is assembled into 676,878 scaffolds with an N50 of 11.80 Mbp. However, in order for the reference genome to be integrated with previous work in the model system, it is necessary to understand the relationship between the scaffolds and the chromosomes they comprise. Therefore, the primary goal of the present study was to assemble the fox chromosomes from the scaffolds of the draft red fox genome assembly. The draft genome was first analyzed to detect bioinformatic errors known to occur in NGS-assembled genomes that might influence the integrity of the chromosome assembly. Based on these findings, the 500 largest scaffolds were assembled into the 17 fox chromosomes (16 autosomes and the X) based both on nucleotide-level synteny among the fox, dog, and cat identified through pairwise alignment of the reference genomes and on interspecies synteny reported in previously developed comparative maps. The result of the current analysis is the development of a new version of the red fox reference genome that will serve as a valuable tool in ongoing research by increasing the resolution at which mapping studies can probe the genetic architecture of complex behavioral phenotypes in the domesticated fox system.
Graduation Semester
2015-8
Type of Resource
text
Permalink
http://hdl.handle.net/2142/88223
Copyright and License Information
Copyright 2015 Halie Rando

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Graduate Dissertations and Theses at Illinois PRIMARY
Graduate Theses and Dissertations at Illinois
Dissertations and Theses - Animal Sciences