Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex

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.

Phylogenetic relationship between Australian Fusarium oxysporum isolates and resolving the species complex using the multispecies coalescent model

“…Sequence variations in this region are due to recombination events caused by parasexualism and this has resulted in three variant type sequences within the mitochondrial genome in FOSC [23]. Mt genome sequences have been used in molecular systematics and biodiversity studies of fungi at various taxonomic levels [24]. Three clades were identified in a phylogenetic analysis of the FOSC using the conserved region of the mt genome in combination with nine nuclear protein coding genes [23].…”

Peer Review #1 of "First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes (v0.1)"

“…Comparative genomics analyses are traditionally reference (Laurent et al, 2017) or pairwise based (Fourie et al, 2013 however, it is difficult to scale to a larger sample size, because every individual has to be compared to every other individual, then the results have to be brought to the same scale.…”

“…Mitochondrial sequences have been used for resolving phylogenetic and evolutionary relationships between fungi at all taxonomic levels (Liu et al, 2009;Avila-Adame et al, 2006;Fourie et al, 2013).…”

Complete mitochondrial genome sequence of lettuce pathogenic fungus, Fusarium oxysporum f. sp. lactucae 16-086

“…Fusarium oxysporum is an ascomycete, soilborne, and pathogenic fungus (Alabouvette and Couteaudier 1992;Fravel et al 2003). Owing to next generation sequencing technologies, more than 60 fungal mitogenomes have been assembled (Pantou et al 2008;Fourie et al 2013;Brankovics et al 2017;Park et al, in preparation). These mitogenomes cover only nine out of around 120 formae speciales, suggesting mitogenomes of more formae speciales should be investigated to understand their genetic diversities as well as host-specificity.…”