Studies in Mycology (2010) 65, 1-60

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M.M. Aveskamp, J. de Gruyter, J.H.C. Woudenberg, G.J.M. Verkley, P.W. Crous (2010)
Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera
Studies in Mycology 65 (1), 1-60
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 ß-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.
Taxonomic novelties: New genus: Boeremia Aveskamp, Gruyter & Verkley. New species: Phoma brasiliensis Aveskamp, Gruyter & Verkley, Ph. bulgarica Aveskamp, Gruyter & Verkley, Ph. dactylidis Aveskamp, Gruyter & Verkley, Ph. dimorpha Aveskamp, Gruyter & Verkley, Ph. longicolla Aveskamp, Gruyter & Verkley, Ph. minor Aveskamp, Gruyter & Verkley, Ph. pedeiae Aveskamp, Gruyter & Verkley, Ph. saxea Aveskamp, Gruyter & Verkley. New varieties: Boeremia exigua var. gilvescens Aveskamp, Gruyter & Verkley, B. exigua var. pseudolilacis Aveskamp, Gruyter & Verkley. New combinations: Boeremia crinicola (Siemasko) Aveskamp, Gruyter & Verkley, B. diversispora (Bubák) Aveskamp, Gruyter & Verkley, B. exigua var. exigua (Desm.) Aveskamp, Gruyter & Verkley, B. exigua var. heteromorpha (Schulzer & Sacc.) Aveskamp, Gruyter & Verkley, B. exigua var. lilacis (Sacc.) Aveskamp, Gruyter & Verkley, B. exigua var. linicola (Naumov & Vassiljevsky) Aveskamp, Gruyter & Verkley, B. exigua var. populi (Gruyter & Scheer) Aveskamp, Gruyter & Verkley, B. exigua var. coffeae (Henn.) Aveskamp, Gruyter & Verkley, B. exigua var. viburni (Roum. ex. Sacc.) Aveskamp, Gruyter & Verkley, B. foveata (Foister) Aveskamp, Gruyter & Verkley, B. lycopersici (Cooke) Aveskamp, Gruyter & Verkley, B. noackiana (Allesch.) Aveskamp, Gruyter & Verkley, B. sambuci-nigrae (Sacc.) Aveskamp, Gruyter & Verkley, B. strasseri (Moesz) Aveskamp, Gruyter & Verkley, B. telephii (Vestergr.) Aveskamp, Gruyter & Verkley, Epicoccum pimprinum (P.N. Mathur, S.K. Menon & Thirum.) Aveskamp, Gruyter & Verkley, E. sorghi (Sacc.) Aveskamp, Gruyter & Verkley, Peyronellaea americana (Morgan-Jones & J.F. White) Aveskamp, Gruyter & Verkley, Pey. alectorolophi (Rehm.) Aveskamp, Gruyter & Verkley, Pey. anserina (Marchal) Aveskamp, Gruyter & Verkley, Pey. arachidicola (Khokhr.) Aveskamp, Gruyter & Verkley, Pey. aurea (Gruyter, Noordel. & Boerema) Aveskamp, Gruyter & Verkley, Pey. calorpreferens (Boerema, Gruyter & Noordel.) Aveskamp, Gruyter & Verkley, Pey. coffeae-arabicae (Aveskamp, Verkley & Gruyter) Aveskamp, Gruyter & Verkley, Pey. curtisii (Berk.) Aveskamp, Gruyter & Verkley, Pey. eucalyptica (Sacc.) Aveskamp, Gruyter & Verkley, Pey. gardeniae (S. Chandra & Tandon) Aveskamp, Gruyter & Verkley, Pey. lethalis (Ellis & Bartholomew) Aveskamp, Gruyter & Verkley, Pey. pomorum var. pomorum (Thüm.) Aveskamp, Gruyter & Verkley, Pey. pomorum var. circinata (Kusnezowa) Aveskamp, Gruyter & Verkley, Pey. pomorum var. cyanea (Jooste & Papendorf) Aveskamp, Gruyter & Verkley, Pey. obtusa (Fuckel) Aveskamp, Gruyter & Verkley, Pey. pinodella (L.K. Jones) Aveskamp, Gruyter & Verkley, Pey. pinodes (Berk. & A. Bloxam) Aveskamp, Gruyter & Verkley, Pey. protuberans (Lév.) Aveskamp, Gruyter & Verkley, Pey. sancta (Aveskamp, Gruyter & Verkley) Aveskamp, Gruyter & Verkley, Pey. subglomerata (Boerema, Gruyter & Noordel.) Aveskamp, Gruyter & Verkley, Pey. zeae-maydis (Arny & R.R. Nelson)Aveskamp, Gruyter & Verkley, Phoma clematidis-rectae (Petr.) Aveskamp, Woudenberg & Gruyter, Ph. noackiana (Allesch.) Aveskamp, Gruyter & Verkley, Stagonosporopsis ajacis (Thüm.) Aveskamp, Gruyter & Verkley, S. andigena (Turkenst.) Aveskamp, Gruyter & Verkley, S. artemisiicola (Hollós) Aveskamp, Gruyter & Verkley, S. astragali (Cooke & Harkn.) Aveskamp, Gruyter & Verkley, S. caricae (Sydow & P. Sydow) Aveskamp, Gruyter & Verkley, S. crystalliniformis (Loer., R. Navarro, M. Lôbo & Turkenst.) Aveskamp, Gruyter & Verkley, S. cucurbitacearum (Fr.) Aveskamp, Gruyter & Verkley, S. dorenboschii (Noordel. & Gruyter) Aveskamp, Gruyter & Verkley, S. heliopsidis (H.C. Greene) Aveskamp, Gruyter & Verkley, S. ligulicola var. ligulicola (K.F. Baker, Dimock & L.H. Davis) Aveskamp, Gruyter & Verkley, S. ligulicola var. inoxydabilis (Boerema) Aveskamp, Gruyter & Verkley, S. loticola (Died.) Aveskamp, Gruyter & Verkley, S. oculo-hominis (Punith.) Aveskamp, Gruyter & Verkley, S. rudbeckiae (Fairm.) Aveskamp, Gruyter & Verkley, S. trachelii (Allesch.) Aveskamp, Gruyter & Verkley, S. valerianellaea (Gindrat, Semecnik & Bolay) Aveskamp, Gruyter & Verkley. New names: Peyronellaea australis Aveskamp, Gruyter & Verkley, Phoma fungicola Aveskamp, Gruyter & Verkley, Ph. novae-verbascicola Aveskamp, Gruyter & Verkley.
(The abstract is excluded from the Creative Commons licence and has been copied with permission by the publisher.)
Full text of article
Database assignments for author(s): Pedro W. Crous

Research topic(s) for pests/diseases/weeds:
identification/taxonomy


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Beneficial Pest/Disease/Weed Crop/Product Country Quarant.


Xenodidymella applanata Raspberry/blackberry (Rubus) Netherlands
Calophoma clematidina Russia (W Asia)
Calophoma clematidina United Kingdom
Calophoma clematidina Netherlands
Leptosphaerulina australis Netherlands
Leptosphaerulina australis Indonesia
Leptosphaerulina trifolii Clover (Trifolium) Netherlands
Phoma macrostoma Netherlands
Phoma macrostoma Switzerland
Phoma macrostoma Germany
Peyronellaea arachidicola Groundnut/peanut (Arachis hypogaea) South Africa
Peyronellaea arachidicola Groundnut/peanut (Arachis hypogaea) Zimbabwe
Peyronellaea curtisii Netherlands
Peyronellaea glomerata Germany
Peyronellaea glomerata Romania
Peyronellaea glomerata Russia (E Asia)
Peyronellaea glomerata Netherlands
Peyronellaea glomerata United Kingdom
Peyronellaea glomerata U.S.A. (NE)
Didymella pinodella Soybean (Glycine max) Hungary
Didymella pinodella Pea (Pisum sativum) Netherlands
Didymella pinodella Clover (Trifolium) U.S.A. (mid N)
Peyronellaea pinodes Pea (Pisum sativum) Belgium
Peyronellaea pinodes Pea (Pisum sativum) Iraq
Peyronellaea pinodes Switzerland
Peyronellaea pinodes Netherlands
Epicoccum sorghinum France
Epicoccum sorghinum Guinea-Bissau
Epicoccum sorghinum India
Epicoccum sorghinum Martinique
Epicoccum sorghinum Papua New Guinea
Epicoccum sorghinum Puerto Rico
Epicoccum sorghinum South Africa
Boeremia exigua var. coffeae Coffee (Coffea) Cameroon
Boeremia exigua Germany
Boeremia exigua Netherlands
Boeremia exigua var. heteromorpha Nerium (genus) France
Boeremia exigua var. heteromorpha Nerium (genus) Italy
Boeremia exigua var. populi Netherlands
Boeremia foveata Potato (Solanum tuberosum) United Kingdom
Boeremia foveata Potato (Solanum tuberosum) Bulgaria
Boeremia diversispora Beans (Phaseolus) Kenya
Boeremia diversispora Beans (Phaseolus) Netherlands
Boeremia telephii Netherlands
Phoma multirostrata India
Phoma multirostrata Netherlands
Phoma costaricensis Nicaragua
Stagonosporopsis caricae Papaya (Carica papaya) Chile (continental)
Stagonosporopsis cucurbitacearum New Zealand
Stagonosporopsis cucurbitacearum Netherlands
Stagonosporopsis tanaceti
Stagonosporopsis loticola New Zealand
Stagonosporopsis lupini Peru
Stagonosporopsis lupini United Kingdom
Stagonosporopsis valerianellae Netherlands
Ascochyta rabiei India
Ascochyta rabiei Syria
Phoma destructiva Guadeloupe
Phoma destructiva Tonga
Ascochyta medicaginicola Czech Republic
Ascochyta medicaginicola Italy
Ascochyta medicaginicola Netherlands
Ascochyta medicaginicola Turkey
Ascochyta medicaginicola U.S.A. (mid N)
Phomatodes nebulosa Austria
Phomatodes nebulosa Netherlands
Didymella rhei New Zealand
Stagonosporopsis andigena Peru
Stagonosporopsis crystalliniformis Tomato (Solanum lycopersicum) Colombia
Phoma novae-verbascicola Verbascum (crop) Netherlands
Stagonosporopsis trachelii