Fungal taxonomists routinely encounter problems when dealing with asexual
fungal species due to poly- and paraphyletic generic phylogenies, and unclear
species boundaries. These problems are aptly illustrated in the genus
Phoma. This phytopathologically significant fungal genus is currently
subdivided into nine sections which are mainly based on a single or just a few
morphological characters. However, this subdivision is ambiguous as several of
the section-specific characters can occur within a single species. In
addition, many teleomorph genera have been linked to Phoma, three of
which are recognised here. In this study it is attempted to delineate generic
boundaries, and to come to a generic circumscription which is more correct
from an evolutionary point of view by means of multilocus sequence typing.
Therefore, multiple analyses were conducted utilising sequences obtained from
28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal
Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the
β-tubulin (TUB) gene region. A total of 324 strains were included in the
analyses of which most belonged to Phoma taxa, whilst 54 to related
pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are
known to have affinities to Phoma. The phylogenetic analysis revealed
that the current Boeremaean subdivision is incorrect from an evolutionary
point of view, revealing the genus to be highly polyphyletic. Phoma
species are retrieved in six distinct clades within the Pleosporales,
and appear to reside in different families. The majority of the species,
however, including the generic type, clustered in a recently established
family, Didymellaceae. In the second part of this study, the
phylogenetic variation of the species and varieties in this clade was further
assessed. Next to the genus Didymella, which is considered to be the
sole teleomorph of Phoma s. str., we also retrieved taxa belonging to
the teleomorph genera Leptosphaerulina and Macroventuria in
this clade. Based on the sequence data obtained, the Didymellaceae
segregate into at least 18 distinct clusters, of which many can be associated
with several specific taxonomic characters. Four of these clusters were
defined well enough by means of phylogeny and morphology, so that the
associated taxa could be transferred to separate genera. Aditionally, this
study addresses the taxonomic description of eight species and two varieties
that are novel to science, and the recombination of 61 additional taxa.
