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Phylogenetic studies of soybean pathogen Phoma species by Bayesian analysis
Published October 20, 2009
53-61

We carried out phylogenetic study analyzing sequences of genetic markers in the taxonomy of Phoma and Phoma-like fungi. Different species of Phoma and Phoma-like fungi occurring on soybean (Phoma pinodella, Phoma sojicola, Phyllosticta sojicola, Phoma exigua var. exigua) are difficult to identy because of their high morphological and symptomati...c similarities.
Twenty-two isolates of nine different Phoma species were obtained from reference culture collections. Seven of them were isolated from soybean, the others were collected from different hosts.
The Phoma isolates were firstly characterised by morphologically, and then we employed a part of the gene responsible for the synthesis of translation elongation factor 1 subunit alpha protein (tef1), ITS region, as well as β-tubulin partial sequences as potential genetic markers to infer
phylogenetic relationships among different Phoma species..Finally, their ITS and tef1 sequences were sequenced and analysed by Bayesian approaches.
According to phylogenetic trees inferred by Bayesian analysis of tef1, ITS and β-tubulin sequences, different Phoma species can be separated proving that these phylogenetic markers are well suited for phylogenetic studies of Phoma species. However, the phylogenetic tree does not support the traditional Phoma sections based on morphological characterization.
Bayesian analyses of the three sequences confirmed that the Phyllosticta sojicola species is clustered with the Phoma exigua var. exigua group and the Phoma sojicola is grouped with Phoma pinodella group. The molecular data provide evidence for reclassification of formerly mentioned soybean pathogens.

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Phylogenetic studies of Phoma species by maximum likelihood analysis
Published October 10, 2008
37-46

The cosmopolitan Phoma genus contains mainly phytopathogenic, opportunistic parasite, and saprophyte fungal species. Up to now the characterization of Phoma species and other taxa of Phoma has so far been determined on the basis of morphology on standardized media, and gene sequence analysis was only used as a confirmative or distinctive comple...ment.
In this study we have tried to study phylogenetic relationships by maximum likelihood method in the Phoma genus. We employed a part of the gene responsible for the synthesis of translation elongation factor 1 subunit alpha protein (tef1) containing both introns and exons, a part of the gene responsible for synthesis of tubulin protein and ITS region containing the internal transcribed spacer regions 1 and 2 and the 5.8S rDNA as potential genetic markers to infer phylogenetic relationships among different Phoma taxa. Twenty-four isolates of eleven different Phoma species were firstly characterised by morphologically, and then their tef1, tubulin and ITS sequences were sequenced and analysed by maximum likelihood method carried out by PAUP*4.0b program. According to constructed phylogenetic trees, the different Phoma taxons are well separated. However these trees do not support the traditional Phoma sections based on morphological characterization.
The maximum likelihood analyses of all three sequences confirmed that the Phyllosticta sojicola species is clustered with the Phoma exigua var. exigua group and the Phoma sojicola is grouped with Phoma pinodella group. The experienced molecular evidences initiate the demand of reclassification of formerly mentioned soybean pathogens. 

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