Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera

Abstract

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.

What if esca disease of grapevine were not a fungal disease?

“…Using GenBank to identify some genera to species level must be treated with caution unless the sequence is derived from an extype strain (Cai et al 2011a,b;Ko Ko et al 2011;Maharachchikumbura et al 2011, Manamgoda et al 2011Tempesta et al 2011;Udayanga et al 2011;Wikee et al 2011;Yang et al 2011). We adopted a 99 % sequence BLAST similarity threshold to determine species names (Gazis et al 2011) because recent studies used more variable gene regions than the ITS to delimitate species that were frequent in our sampling (Aveskamp et al 2009;Aveskamp et al 2010;Chaverri et al 2011;Schubert et al 2007).…”

Taxonomic circumscription and phylogenetics of novel didymellaceous taxa with brown muriform spores

“…Newly generated sequences from two Microsphaeropsis isolates (MFLU 16-0100 and MFLU 16-0097) grouped with isolates currently circumscribed as Microsphaeropsis olivacea and M. proteae (de Gruyter et al 2009, Aveskamp et al 2010, Crous et al 2011, Verkley et al 2014, Chen et al 2015. These taxa formed an isolated clade (Clade A , Fig 1) within Didymellaceae, but poorly supported in multi-gene analyses (69% in ML, <60 % in MP and <0.95 in BI).…”

Effect of sorghum seed treatment in Burkina Faso varies with baseline crop performance and geographical location

“…It was demonstrated that the positive effect of the plant extract was specific compared to soaking of seeds in pure water (Zida et al, 2012). The biological mechanism of action of E. alba extract is still unknown, but a dose dependent inhibition of the fungal pathogen, Epicoccum sorghinum (previously Phoma sorghina or Leptosphaeria sacchari, Aveskamp et al, 2010) was demonstrated by Zida et al (2012). Epicoccum sorghinum is highly abundant on seeds of sorghum in Burkina Faso (Zida et al, 2008b).…”