Abstract
BackgroundThe availability of mitochondrial genomes has allowed for the resolution of numerous questions regarding the evolutionary history of fungi and other eukaryotes. In the Gibberella fujikuroi species complex, the exact relationships among the so-called “African”, “Asian” and “American” Clades remain largely unresolved, irrespective of the markers employed. In this study, we considered the feasibility of using mitochondrial genes to infer the phylogenetic relationships among Fusarium species in this complex. The mitochondrial genomes of representatives of the three Clades (Fusarium circinatum, F. verticillioides and F. fujikuroi) were characterized and we determined whether or not the mitochondrial genomes of these fungi have value in resolving the higher level evolutionary relationships in the complex.ResultsOverall, the mitochondrial genomes of the three species displayed a high degree of synteny, with all the genes (protein coding genes, unique ORFs, ribosomal RNA and tRNA genes) in identical order and orientation, as well as introns that share similar positions within genes. The intergenic regions and introns generally contributed significantly to the size differences and diversity observed among these genomes. Phylogenetic analysis of the concatenated protein-coding dataset separated members of the Gibberella fujikuroi complex from other Fusarium species and suggested that F. fujikuroi (“Asian” Clade) is basal in the complex. However, individual mitochondrial gene trees were largely incongruent with one another and with the concatenated gene tree, because six distinct phylogenetic trees were recovered from the various single gene datasets.ConclusionThe mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex are remarkably similar to those of the previously characterized Fusarium species and Sordariomycetes. Despite apparently representing a single replicative unit, all of the genes encoded on the mitochondrial genomes of these fungi do not share the same evolutionary history. This incongruence could be due to biased selection on some genes or recombination among mitochondrial genomes. The results thus suggest that the use of individual mitochondrial genes for phylogenetic inference could mask the true relationships between species in this complex.
Highlights
The availability of mitochondrial genomes has allowed for the resolution of numerous questions regarding the evolutionary history of fungi and other eukaryotes
The average GC content of the three Gibberella fujikuroi complex (GFC) genomes were 31.4%, 32.6% and 32.4%, respectively, which fall within the range of what was found for the other Fusarium mt genomes [22]
Half (50.5%) of the F. circinatum mt genome comprised of protein coding sequences, which is comparable to the 57.6% found in the F. oxysporum mt genome
Summary
The availability of mitochondrial genomes has allowed for the resolution of numerous questions regarding the evolutionary history of fungi and other eukaryotes. The mitochondrial genomes of representatives of the three Clades (Fusarium circinatum, F. verticillioides and F. fujikuroi) were characterized and we determined whether or not the mitochondrial genomes of these fungi have value in resolving the higher level evolutionary relationships in the complex. The mt genome is considered to be an ideal region to study eukaryotic evolution [2] This is linked to its ancestral origins, and because of its accelerated rate of evolution, which is associated with a high copy number that allows mutations to occur without lethal impact [6]. It is not surprising that mt genomes have been used in various phylogenetic and comparative studies to resolve and/or determine evolutionary relationships between or among eukaryotes at all taxonomic levels e.g [10,11]. Partial or whole mt genome sequence data have been used to resolve relationships among various members of the Basidiomycota [12,13,14], and in the Ascomycota among classes such as Schizosaccharomycetes [15], Dothideomycetes [16], Eurotiomycetes [17], as well as Sordariomycetes [18,19,20,21,22]
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