Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the evolutionary histories of multiple genes

<p>Abstract</p> <p>Background</p> <p>Species of the <it>Fusarium </it>genus are important fungi which is associated with health hazards in human and animals. The taxonomy of this genus has been a subject of controversy for many years. Although many researchers have applied molecular phylogenetic analysis to examine the taxonomy of <it>Fusarium </it>species, their phylogenetic relationships remain unclear only few comprehensive phylogenetic analyses of the <it>Fusarium </it>genus and a lack of suitable nucleotides and amino acid substitution rates. A previous stugy with whole genome comparison among <it>Fusairum </it>species revealed the possibility that each gene in <it>Fusarium </it>genomes has a unique evolutionary history, and such gene may bring difficulty to the reconstruction of phylogenetic tree of <it>Fusarium</it>. There is a need not only to check substitution rates of genes but also to perform the exact evaluation of each gene-evolution.</p> <p>Results</p> <p>We performed phylogenetic analyses based on the nucleotide sequences of the rDNA cluster region (rDNA cluster), and the β-tubulin gene (<it>β-tub</it>), the elongation factor 1α gene (<it>EF-1α</it>), and the aminoadipate reductase gene (<it>lys2</it>). Although incongruence of the tree topologies between <it>lys2 </it>and the other genes was detected, all genes supported the classification of <it>Fusarium </it>species into 7 major clades, I to VII. To obtain a reliable phylogeny for <it>Fusarium </it>species, we excluded the <it>lys2 </it>sequences from our dataset, and re-constructed a maximum likelihood (ML) tree based on the combined data of the rDNA cluster, <it>β-tub</it>, and <it>EF-1α</it>. Our ML tree indicated some interesting relationships in the higher and lower taxa of <it>Fusarium </it>species and related genera. Moreover, we observed a novel evolutionary history of <it>lys2</it>. We suggest that the unique tree topologies of <it>lys2 </it>are not due to an analytical artefact, but due to differences in the evolutionary history of genomes caused by positive selection of particular lineages.</p> <p>Conclusion</p> <p>This study showed the reliable species tree of the higher and lower taxonomy in the lineage of the <it>Fusarium </it>genus. Our ML tree clearly indicated 7 major clades within the <it>Fusarium </it>genus. Furthermore, this study reported differences in the evolutionary histories among multiple genes within this genus for the first time.</p