Student thesis: Doctoral Thesis › Doctor of Philosophy
|Award date||25 Nov 2015|
Genomes undergo mutation during evolution. Out of several mutational events, large-scale mutations, called genome rearrangements, mainly contribute to large-scale structural changes in chromosomes. My study of genome rearrangements mainly concentrates on identifying chromosomal evolutionary breakpoint regions and connects these to changes gained by each species during the course of evolution. In this thesis, I first focused on comparative genome analysis of seven mammalian genomes and discovered 192 evolutionary breakpoints in the pig genome. Subsequently, an extensive study demonstrated how chromosomal rearrangements produced variations in the gene networks potentially used by natural selection for adaptation. Thereafter, I developed a novel computational tool which uses a statistical method to find breakpoints in chromosomes with respect to various genome attributes, such as genome size, assembly type, and the phylogenetic relationship between species. The published cattle EBR dataset was used to test the algorithm, in which I was able to classify upto 95.55% of cattle specific EBRs. The comparative analysis of avian genomes demonstrates that there are lower rates of chromosome evolution as well as the presence of lower fractions of transposable elements in bird genomes compared to mammals. Our study revealed enrichment for Gene Ontology terms related to regulation of gene expression and biosynthetic processes in bird, crocodile and turtle HSBs. The archosaurian HSBs were found enriched for genes that are responsible for the similar retina structures in birds and crocodiles, while the avian HSBs contain genes involved in the bird skeleton and limb development. Moreover, the analysis of gene content in and around avian EBRs revealed enrichments for genes related to lineage-specific phenotypes, such as the GO terms “regionalisation” in the Adelie penguin and “forebrain development” in the Budgerigar. Our findings shed light on mechanisms underlying adaptation, development, and evolution at the genomic level.
Thesis, 3 MB, PDF
Show more files.. Show less files..
Thesis, 3 MB, PDF
|This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License|