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

Abstract

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

Early PCR-based detection of Fusarium culmorum, F. graminearum, F. sporotrichioides and F. poae on stem bases of winter wheat throughout Poland

“…These relationships are likely to be explained by the influence of other associated factors, i.e., forecrop and date of sowing that emerged from further analyses of samples. However, a very interesting co-incidence was also noted in these correlations of Fusarium species from the same Fusarium sections: Discolor (F. graminearum and F. culmorum) and Sporotrichiella (F. poae and F. sporotrichioides) (Watanabe et al 2011).…”

454 Pyrosequencing Analysis of Fungal Assemblages from Geographically Distant, Disparate Soils Reveals Spatial Patterning and a Core Mycobiome

“…Blast results were inspected manually to remove inconsistencies: a match with a single sequence assigned to a genus represented by several species in the reference database was not considered, since we suspected misidentification of the database sequence. As the ITS region has limited value for differentiating species within Fusarium and Penicillium [66,88], OTUs assigned to these taxa were only identified to the genus level.…”

Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches

“…The literature presents various methods for the characterization of fungal flora. These include the determination of the growth parameters (Steinberg et al, 1997a), analysis of the diversity of β-tubulin sequences (Watanabe et al, 2011), ribosomal genes sequencing (Kodsueb et al, 2006;Crous et al, 2007;Schroers et al, 2009), intergenic 18S-28S internal transcribed spacer (ITS) sequencing (Camara et al, 2002;Braun et al, 2003;Pryor and Bigelow, 2003;Kwasna et al, 2006;Manamgoda et al, 2012), multilocus analysis (Zhang et al, 2009a), and single sequence repeat (SSR) genotyping (Wang et al, 2010). Further methods include terminal restriction fragment length polymorphism (T-RFLP) (Dickie and FitzJohn, 2007), amplified ribosomal DNA restriction analysis (ARDRA) (Sutthisa et al, 2010), as well as ribosomal intergenic spacer analysis (RISA) (Sigler and Zeyer, 2002).…”