Download Abstract The phenomena of gene fusion and fission occur

Abstract
The phenomena of gene fusion and fission occur throughout evolution in the fungal
kingdom during which ORFs may be fuse or split to yield a new gene product or two
new gene products that are free to evolve independently. Previous works have
suggested that gene fissions and fusions may suggest relationship identification
markers in taxonomic clades. We intend to expand on this and identify fused triplets,
which are two otherwise unrelated genes that both share homology with a larger gene.
We intend to identify the number of composites and the relationship of any conserved
phenomena with each other, with neighbouring genes and with the evolutionary
timeline across 114 fungal genomes to investigate the frequency of fusion and fission
events of particular triplets by utilizing comparative genomic analysis and
conservative phylogenetic tree construction. We are interested in observing what
evolutionary benefits arose from gene fusion and fission and the associated effects
conferred upon these species. We hope to identify fusion and fission prone genes and
their associated protein domains and to link them to their environmental conditions,
which may be the case for secondary metabolite genes. We are interested in
investigating if any particular species, genus or family are more susceptible to gene
fusion or gene fission events and also if any gene families are more susceptible to
undergoing these events. We would be particularly interested to see if genes from a
prokaryotic origin are more susceptible to these events than eukaryotic originating
genes or vice versa.
We require an all-against-all BLAST search of the 114 genomes, high throughput
graph structure analysis, phylogenetic analysis and protein domain identification. We
have estimated that this will cost approximately 400,000 hours in total, which will be
divided across 800 nodes. We hold a class C licence however this is insufficient for
the amount of data we wish to analyse. We wish to apply for a class B licence,
effective immediately. Future work for the PhD is likely to require several analyses of
datasets of similar size from animal, plant, prokaryotic, and viral origins.