Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences

DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochrome c oxidase 1 (CO1) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence divergences in this gene region for 38 fungal taxa with full CO1 sequences. Because these results suggested that CO1 could be effective in species recognition, we designed primers for a 545-bp fragment of CO1 and generated sequences for multiple strains from 58 species of Penicillium subgenus Penicillium and 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370 Penicillium strains. Representatives from 38 of 58 species formed cohesive assemblages with distinct CO1 sequences, and all cases of sequence sharing involved known species complexes. CO1 sequence divergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or β-tubulin sequences (BenA). CO1 divergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values for BenA (14.4%). Although the latter gene delivered higher taxonomic resolution, the amplification and alignment of CO1 was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.

/pdf/prospects-for-fungus-identification-using-co1-dna-barcodes-2u9dr7nhye.pdf

Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case.

The current status of species recognition and identification in Aspergillus

The phylogenetic relationships of 51 iso- lates representing 27 species of Phytophthora were as- sessed by sequence alignment of 568 bp of the mi- tochondrially encoded cytochrome oxidase II gene. A total of 1299 bp of the cytochrome oxidase I gene also were examined for a subset of 13 species. The cox II gene trees constructed by a heuristic search, based on maximum parsimony for a bootstrap 50% majority-rule consensus tree, revealed 18 species grouping into seven clades and nine species unaffil- iated with a specific clade. The phylogenetic relation- ships among species observed on cox II gene trees did not exhibit consistent similarities in groupings for morphology, pathogenicity, host range or tem- perature optima. The topology of cox I gene trees, constructed by a heuristic search based on maximum parsimony for a bootstrap 50% majority-rule consen- sus tree for 13 species of Phytophthora, revealed 10 species grouping into three clades and three species unaffiliated with a specific clade. The groupings in general agreed with what was observed in the cox II tree. Species relationships observed for the cox II gene tree were in agreement with those based on ITS regions, with several notable exceptions. Some of these differences were noted in species in which the same isolates were used for both ITS and cox II anal- ysis, suggesting either a differential rate of evolution- ary divergence for these two regions or incorrect as- sumptions about alignment of ITS sequences. Anal- ysis of combined data sets of ITS and cox II sequences generated a tree that did not differ substantially from analysis of ITS data alone, however, the results of a partition homogeneity test suggest that combining data sets may not be valid.

Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes

Mycotoxigenic Fusarium species in animal feed

Restriction fragment length polymorphisms (RFLPs) were used to assess genetic diversity of mitochondrial DNA (mtDNA) among standard isolates of seven lineages of Fusarium graminearum. The mtDNA patterns within each lineage were very similar (>89%), whereas significant differences were observed between the isolates belonging to different lineages, with the exception of lineages 1 and 4 where strong similarity was found between the RFLPs. Analysis of different band patterns resulted in characteristic HhaI and HaeIII bands that were suitable for identification of members of lineages 7, 6, 5, 3 and 2. Investigation of lineage distribution of 144 European isolates revealed that 142 belong to lineage 7. These data, therefore, confirmed the hypothesis that members of lineage 7 are predominant in Europe. Further analysis of isolates belonging to lineage 7 resulted in five haplotypes. These haplotypes have arisen as different combinations of three RFLP patterns for both HaeIII and HhaI restriction enzymes. Two isolates from Hungary, however, shared the same mtDNA RFLP profiles with a standard isolate of lineage 3, indicating that members of lineage 3, at a lower frequency, may also occur in Europe.

Mitochondrial DNA diversity and lineage determination of European isolates of Fusarium graminearum (Gibberella zeae)

A total of 36 single-lesion isolates were collected from 9 crops of potato and 13 of tomato in different regions of Hungary in the past decade, particularly in 1998. These were analysed for mating type, sensitivity to metalaxyl, allozyme genotype at glucose-6-phosphate isomerase and peptidase loci and genotype at 24 loci detected using the multilocus RFLP probe RG57. The ratios of the mating types A1 to A2 were 8 : 9 and 4 : 15 among isolates recovered from potato and tomato, respectively. Resistance to metalaxyl was found more frequently among isolates from potato and in the A1 mating type. The populations were not clearly differentiated on the basis of host origin. All isolates were homozygous (100/100) at the locus for glucose-6-phosphate isomerase. Unlike in other European countries, the most common peptidase allele was 96. Genotypes at the peptidase locus were 96/96 (50%), 96/100 (27.7%) and 100/100 (16.6%). In addition, one isolate from 1993 and another from 1998, were defined as 83/96, a genotype that had not been described elsewhere. The 18 RG57 fingerprints that were observed among 36 isolates, with one exception, seem to be unique to Europe. On the basis of combined genotypic traits, 20 multilocus genotypes were designated. These data, which reveal a remarkable variability with unique genotypes of the late blight pathogen, suggest that migration and sexual and/or asexual recombination have a role in the recent evolution of the pathogen in Hungary.

Characterisation of Isolates of Phytophthora infestans From Hungary

Cryptic subspecies and beauvericin production by Fusarium subglutinans from Europe.

Phenotypic and molecular characterization of species hybrids derived from induced fusion of zoospores of Phytophthora capsici and Phytophthora nicotianae

M. Láday

Papers

Mitochondrial DNA diversity and lineage determination of European isolates of Fusarium graminearum (Gibberella zeae)

Characterisation of Isolates of Phytophthora infestans From Hungary

Cryptic subspecies and beauvericin production by Fusarium subglutinans from Europe.

Phenotypic and molecular characterization of species hybrids derived from induced fusion of zoospores of Phytophthora capsici and Phytophthora nicotianae

Isozyme evidence for two groups of Fusarium graminearum.