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Phylogenetic trees of Byssochlamys spp. and relaled species inferred from sequences of the 18S rDNA (a), 26/28S rDNA D2 region (b) and lys2 (c)
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Comparative sequence analysis was performed on the 18S rRNA gene (1,676 bp), 26/28S rRNA gene D2 region (321 bp) and lys2 (997 bp) to evaluate the gene index for rapid, accurate and convenient identification of Byssochlamys spp. and related species. The results showed that 26 strains (11 species) of the clade could be identified or grouped by means...
Citations
... O'Donnell et al. [14] showed that there are species complexes including more than 2 species, such as the Gibberella fujikuroi species complex. O'Donnell et al. [14] and O'Donnell and Cigelnik [14,17] showed that some sections proposed by morphological studies form paraphyletic or polyphyletic groups, such as Sporotrichiella and Discolor. This study supported their results. ...
... Although our ML tree was constructed with a high resolution, the relationships among species that together form a complex could not be resolved. Previous molecular phylogenetic analyses have suggested that a species of the Liseola section, defined by traditional taxonomy based on the morphological species concept, actually includes multiple species, and that the re-defined novel species, which are recognized mainly by mating types, constitute the Gibberella fujikuroi species complex1516171819202122232425262728. The ML tree obtained in this study (Figure 6) demonstrates convoluted, nested structures of species within the Liseola section. ...
... For PCR amplification other than that for ITS1, 5.8S rDNA, and 28S rDNA, we used the following primer pairs: FF1 (5'-GTTAAAAAGCTCGTAGTT- GAAC-3'; [39])/FR1 (5'-CTCTCAATCTGTCAATCC TTATT-3'; [39]) for 18S rDNA; Btu-F-F01 (5'-CAGACC GGTCAGTGCGTAA-3')/Btu-F-R01 (5'-TTGGGGTCG AACATCTGCT-3') for b-tub; EF-1 (5'-ATGGGTAAG- GARGACAAGAC-3'; [40] )/EF-2 (5'-GGARGTACCAGT- SATCATGTT-3'; [40]) for EF-1a; and 2 primer pairs of Fulys2-F03mix (5'-CTTTGTTGGTGATGTTCTSA-3')/ Fulys2-R01 (5'-TGGTAGGTCCGATATCGGT-3') and Fulys2-F04mix (5'-GCYATGGGDCARATYCTKGT -3')/ Fulys2-R04mix (5'-CGGYTCYTCRTTRCGRTCTCT-3') for lys2. The primer pairs for b-tub and lys2 were designed based on sequences derived from primers used in previous studies, respectively [16,17]. They were designed to amplify the genes effectively. ...
Species 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.
We 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.
This 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.
... 4,6,8 It was also indicated that the aminoadipate reductase gene (lys2) was a good phylogenetic marker for relationships both among genera of fungi 9 and among species of the genus Byssochlamys and its related genera with higher evolutionary rate than other frequently used genes. 10 In the present study, we analysed sequences of four parts of the rDNA cluster region, βtub, and lys2 to specify the gene(s) appropriate for identifying Fusarium isolates. We focused on the identification by an easy and rapid method with the nucleotide sequence homology against sequences in the database. ...
Members of the genus Fusarium are well known as one of the most important plant pathogens causing food spoilage and loss worldwide. Moreover, they are associated with human and animal diseases through contaminated foods because they produce mycotoxins. To control fungal hazards of plants, animals and humans, there is a need for a rapid, easy and accurate identification system of Fusarium isolates with molecular methods.
To specify genes appropriate for identifying isolates of various Fusarium species, we sequenced the 18S rRNA gene (rDNA), internal transcribed spacer region 1, 5.8S rDNA, 28S rDNA, β-tubulin gene (β-tub), and aminoadipate reductase gene (lys2), and subsequently calculated the nucleotide sequence homology with pair-wise comparison of all tested strains and inferred the ratio of the nucleotide substitution rates of each gene. Inter-species nucleotide sequence homology of β-tub and lys2 ranged from 83.5 to 99.4% and 56.5 to 99.0%, respectively. The result indicated that sequence homologies of these genes against reference sequences in a database have a high possibility of identifying unknown Fusarium isolates when it is more than 99.0%, because these genes had no inter-species pair-wise combinations that had 100% homologies. Other markers often showed 100% homology in inter-species pair-wise combinations. The nucleotide substitution rate of lys2 was the highest among the six genes.
The lys2 is the most appropriate genetic marker with high resolution for identifying isolates of the genus Fusarium among the six genes we examined in this study.
... For DNA from yeast cells and ascomycetous molds, forward primer FF1 (59-GTT AAA AAG CTC GTA GTT GAA C-39) and reverse primer FR1 (59-CTC TCA ATC TGT CAA TCC TTA TT-39) were used (32). For DNA from zygomycetous molds, forward primer P1 (59-ATC TGG TTG ATC CTG CCA-39) and reverse primer Fun-R1 (59-TTG TTA CGA CTT TTA CTT CCT CT-39) were used (30). These primer pairs were designed to amplify specific fragments (of 630 and 1,730 bp, respectively) in two regions of the 18S rRNA gene, which is one of the most widely used genes in systematics studies based on molecular biological techniques. ...
To identify a rapid method for extracting a large amount of DNA from fungi associated with food hygiene, extraction methods were compared using fungal pellets formed rapidly in liquid media. Combinations of physical and chemical methods or commercial kits were evaluated with 3 species of yeast, 10 species of ascomycetous molds, and 4 species of zygomycetous molds. Bead grinding was the physical method, followed by chemical methods involving sodium dodecyl sulfate (SDS), cetyl trimethyl ammonium bromide (CTAB), and benzyl chloride and two commercial kits. Quantity was calculated by UV absorbance at 260 nm, quality was determined by the ratio of UV absorbance at 260 and 280 nm, and gene amplifications and electrophoresis profiles of whole genomes were analyzed. Bead grinding with the SDS method was the most effective for DNA extraction for yeasts and ascomycetous molds, and bead grinding with the CTAB method was most effective with zygomycetous molds. For both groups of molds, bead grinding with the CTAB method was the best approach for DNA extraction. Because this combination also is relatively effective for yeasts, it can be used to extract a large amount of DNA from a wide range of fungi. The DNA extraction methods are useful for developing gene indexes to identify fungi with molecular techniques, such as DNA fingerprinting.
