Reproductive Isolation, in Individuals and During Evolution, as Result of Gross Genomic Rearrangement in Pigs, Birds and Dinosaurs

Chromosomal (karyotypic) analysis in animals is performed for three primary reasons: to diagnose genetic disease; to map genes to their place in the genome and to retrace evolutionary events by cross species comparison. Technology for analysis has progressed from chromosome banding (cytogenetics), to fluorescence in-situ hybridisation (FISH - molecular cytogenetics) through to microarrays and ultimately whole genome sequence analysis (cytogenomics or chromonomics). Indeed, the past 10-15 years has seen a revolution in whole genome sequencing, first with the human genome project, followed by those of key model and agricultural species and, more recently, ~60 de novo avian genome assemblies. Whole genome analysis provides detailed insight into the biology of chromosome rearrangements that occur both in individuals (for diagnostic purposes) and at an evolutionary level. It permits the study of gene mapping, trait linkage, phylogenomics, and gross genomic organisation and change. An essential pre-requisite however is an unbroken length of contiguous DNA sequence along the length of each chromosome. Most recent de novo genome assemblies fall short of this level of resolution producing lengths of contiguous sequence that are sub-chromosomal in size (scaffolds).

Chromosome rearrangements can affect reproductive capability at an individual level (causing reduced fertility) and at a population level leading to reproductive isolation and subsequent speciation. The purpose of this thesis was to implement a step change in the combination of FISH technology with genome sequence data to provide greater insight into the nature of chromosomal rearrangement at an individual and evolutionary level. It therefore had four specific aims:

The first was to isolate sub-telomeric sequences from the pig, cattle and chicken genome assemblies to develop a tool for the rapid screening of chromosome rearrangements. Now routinely used for porcine translocation screening (and in the future bovine screening), development work revealed serious integrity errors in the pig genome. The second aim was to isolate evolutionary conserved sequences from avian chromosomes to create a means of screening for macro-and microchromosomal rearrangements in birds. Results confirmed the hypothesis that microchromosomal rearrangements were rare in birds, except for previously known whole chromosomal fusions. The third was to use the above tools to complete scaffold based genome assemblies in two key avian species - the peregrine falcon and the pigeon. Finally, bioinformatic tools were used to infer the overall genome structure of hypothetical saurian and avian ancestors. Retracing of the evolutionary changes that occurred up until the emergence of birds allowed an assessment of chromosome evolution along the saurischia-maniraptora- avialae lineage. Analysis of evolutionary breakpoint regions (EBRs) allowed testing of the hypothesis that the ontology of genes within EBRs corresponded to measurable phenotypic change in the lineage under investigation. An enrichment of genes associated with body height corresponded to rapid size change in the dinosaur linage that led to modern birds.

Taken together, these results paint a picture of a genome that, from about 260 million years ago formed a 'signature' highly successful avian-dinosaur karyotype that remained largely unchanged interchromosomally to the present day. These results represent significant insight into amniote genomic organization with the added benefit of developing tools that are widely applicable and transferrable for commercial animal breeding, for constructing de novo genome assemblies and for reconstructing, by inference, the overall genomic structure and evolution of extinct animals.