Durrens P, Nikolski M, Sherman D. Fusion and fission of genes define a metric between fungal genomes.
PLoS Comput Biol 2008;
4:e1000200. [PMID:
18949021 PMCID:
PMC2557144 DOI:
10.1371/journal.pcbi.1000200]
[Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Accepted: 09/05/2008] [Indexed: 12/19/2022] Open
Abstract
Gene fusion and fission events are key mechanisms in the evolution of gene architecture, whose effects are visible in protein architecture when they occur in coding sequences. Until now, the detection of fusion and fission events has been performed at the level of protein sequences with a post facto removal of supernumerary links due to paralogy, and often did not include looking for events defined only in single genomes. We propose a method for the detection of these events, defined on groups of paralogs to compensate for the gene redundancy of eukaryotic genomes, and apply it to the proteomes of 12 fungal species. We collected an inventory of 1,680 elementary fusion and fission events. In half the cases, both composite and element genes are found in the same species. Per-species counts of events correlate with the species genome size, suggesting a random mechanism of occurrence. Some biological functions of the genes involved in fusion and fission events are slightly over- or under-represented. As already noted in previous studies, the genes involved in an event tend to belong to the same functional category. We inferred the position of each event in the evolution tree of the 12 fungal species. The event localization counts for all the segments of the tree provide a metric that depicts the “recombinational” phylogeny among fungi. A possible interpretation of this metric as distance in adaptation space is proposed.
One consequence of genome remodelling in evolution is the modification of genes, either by fusion with other genes, or by fission into several parts. By tracking the mathematical relations between groups of similar genes, rather than between individual genes, we can paint a global picture of remodelling across many species simultaneously. The strengths of our method are that it allows us to include highly redundant eukaryote genomes, and that it avoids alignment artifacts by representing each group of similar genes by a mathematical model. Applying our method to a set of fungal genomes, we confirmed first that the number of fusion/fission events is correlated with genome size, second that the fusion to fission ratio favors fusions, third that the set of events is not saturated, and fourth that while genes assembled in a fusion tend to have the same biochemical function, there appears to be little bias for the functions that are involved. Indeed, fusion and fission events are landmarks of random remodelling, independent of mutation rate: they define a metric of “recombination distance.” This distance lets us build a genome evolution history of species and may well be a better measure than mutation distance of the process of adaptation.
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