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.
Highlights
As the number of complete genome sequences increases, comparative genomics unveils the mechanisms of gene and genome evolution
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
We present here a large scale computation method for detecting gene fusion and fission events in eukaryote genomes, even when they have a noticeable amount of internal gene redundancy
Summary
As the number of complete genome sequences increases, comparative genomics unveils the mechanisms of gene and genome evolution. Duplication, sequence divergence, and recombination are the major mechanisms at work in gene evolution [1]. Recombinational events such as translocation, inversion or segmental duplication can create accidental fusion of DNA sequences associated with different genes, or the fission of a gene into several parts. These events can create new genes from already existing parts, or reciprocally shuffle genes into sub-parts across a genome. These rare events participate in the evolutionary history of the species, and must be taken into account in genome rearrangement models
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