title: Resolving the Phoma enigma.
abstract: The Didymellaceae was established in 2009 to accommodate Ascochyta, Didymella and Phoma, as well as several related phoma-like genera. The family contains numerous plant pathogenic, saprobic and endophytic species associated with a wide range of hosts. Ascochyta and Phoma are morphologically difficult to distinguish, and species from both genera have in the past been linked to Didymella sexual morphs. The aim of the present study was to clarify the generic delimitation in Didymellaceae by combing multi-locus phylogenetic analyses based on ITS, LSU, rpb2 and tub2, and morphological observations. The resulting phylogenetic tree revealed 17 well-supported monophyletic clades in Didymellaceae, leading to the introduction of nine genera, three species, two nomina nova and 84 combinations. Furthermore, 11 epitypes and seven neotypes were designated to help stabilise the taxonomy and use of names. As a result of these data, Ascochyta, Didymella and Phoma were delineated as three distinct genera, and the generic circumscriptions of Ascochyta, Didymella, Epicoccum and Phoma emended. Furthermore, the genus Microsphaeropsis, which is morphologically distinct from the members of Didymellaceae, grouped basal to the Didymellaceae, for which a new family Microsphaeropsidaceae was introduced.
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Rd, Chaoyang District, Beijing 100101, China.
authors.forename: Q
authors.initials: Q
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Rd, Chaoyang District, Beijing 100101, China.
authors.forename: J R
authors.initials: JR
authors.lastname: Jiang
authors.affiliation: College of Agriculture and Biotechnology, China Agricultural University, No. 2 West Yuanmingyuan Rd, Haidian District, Beijing 100193, China.
authors.forename: G Z
authors.initials: GZ
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Rd, Chaoyang District, Beijing 100101, China.
authors.forename: L
authors.initials: L
authors.lastname: Cai
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: P W
authors.initials: PW
authors.lastname: Crous
keywords: All. minor (Aveskamp et al.) Q. Chen & L. Cai; All. piperis (Tassi) Q. Chen & L. Cai; All. tropica (R. Schneid. & Boerema) Q. Chen & L. Cai; All. zantedeschiae (Dippen.) Q. Chen & L. Cai; Allophoma Q. Chen & L. Cai; Allophomalabilis (Sacc.) Q. Chen & L. Cai; Allophomanicaraguensis Q. Chen & L. Cai; As. medicaginicola var. macrospora (Boerema et al.) Q. Chen & L. Cai; As. nigripycnidia (Boerema et al.) Q. Chen & L. Cai; As. phacae (Corbaz) Q. Chen & L. Cai; As. versabilis (Boerema et al.) Q. Chen & L. Cai; Ascochyta; Ascochytaherbicola (Wehm.) Q. Chen & L. Cai; Ascochytamedicaginicola var. medicaginicola Q. Chen & L. Cai; Boeremialilacis (Sacc.) Q. Chen & L. Cai; Ca. clematidina (Thüm.) Q. Chen & L. Cai; Ca. clematidis-rectae (Petr.) Q. Chen & L. Cai; Ca. complanata (Tode) Q. Chen & L. Cai; Ca. glaucii (Brunaud) Q. Chen & L. Cai; Ca. vodakii (E. Müll.) Q. Chen & L. Cai; Calophoma Q. Chen & L. Cai; Calophomaaquilegiicola (M. Petrov) Q. Chen & L. Cai; D. aliena (Fr.) Q. Chen & L. Cai; D. americana (Morgan-Jones & J.F. White) Q. Chen & L. Cai; D. anserina (Marchal) Q. Chen & L. Cai; D. aurea (Gruyter et al.) Q. Chen & L. Cai; D. bellidis (Neerg.) Q. Chen & L. Cai; D. boeremae (Gruyter) Q. Chen & L. Cai; D. calidophila (Aveskamp et al.) Q. Chen & L. Cai; D. chenopodii (P. Karst. & Har.) Q. Chen & L. Cai; D. coffeae-arabicae (Aveskamp et al.) Q. Chen & L. Cai; D. curtisii (Berk.) Q. Chen & L. Cai; D. dactylidis (Aveskamp et al.) Q. Chen & L. Cai; D. dimorpha (Aveskamp et al.) Q. Chen & L. Cai; D. eucalyptica (Sacc.) Q. Chen & L. Cai; D. gardeniae (S. Chandra & Tandon) Q. Chen & L. Cai; D. glomerata (Corda) Q. Chen & L. Cai; D. heteroderae (Boerema et al.) Q. Chen & L. Cai; D. longicolla (Aveskamp et al.) Q. Chen & L. Cai; D. mascrostoma (Mont.) Q. Chen & L. Cai; D. maydis (Arny & R.R. Nelson) Q. Chen & L. Cai; D. microchlamydospora (Aveskamp & Verkley) Q. Chen & L. Cai; D. molleriana (G. Winter) Q. Chen & L. Cai; D. musae (P. Joly) Q. Chen & L. Cai; D. negriana (Thüm.) Q. Chen & L. Cai; D. nigricans (P.R. Johnst. & Boerema) Q. Chen & L. Cai; D. pedeiae (Aveskamp et al.) Q. Chen & L. Cai; D. pinodella (L.K. Jones) Q. Chen & L. Cai; D. pomorum (Thüm.) Q. Chen & L. Cai; D. protuberans (Lév.) Q. Chen & L. Cai; D. rhei (Ellis & Everh.) Q. Chen & L. Cai; D. rumicicola (Boerema & Loer.) Q. Chen & L. Cai; D. sancta (Aveskamp et al.) Q. Chen & L. Cai; D. subglomerata (Boerema et al.) Q. Chen & L. Cai; D. subherbarum (Gruyter et al.) Q. Chen & L. Cai; D. viburnicola (Oudem.) Q. Chen & L. Cai; Didymella; Didymellaacetosellae (A.L. Sm. & Ramsb.) Q. Chen & L. Cai; Didymellasenecionicola Q. Chen & L. Cai; E. draconis (Berk. ex Cooke) Q. Chen & L. Cai; E. henningsii (Sacc.) Q. Chen & L. Cai; E. huancayense (Turkenst.) Q. Chen & L. Cai; E. plurivorum (P.R. Johnst.) Q. Chen & L. Cai; Epicoccumbrasiliense (Aveskamp et al.) Q. Chen & L. Cai; H. nobilis (Kabát & Bubák) Q. Chen & L. Cai; H. novae-verbascicola (Aveskamp et al.) Q. Chen & L. Cai; H. poolensis (Taubenh.) Q. Chen & L. Cai; H. sylvatica (Sacc.) Q. Chen & L. Cai; Heterophoma Q. Chen & L. Cai; Heterophomaadonidis (Moesz) Q. Chen & L. Cai; Microsphaeropsidaceae Q. Chen, L. Cai & Crous; Multi-locus phylogeny; Neoa. europaea (Punith) Q. Chen & L. Cai; Neoa. exitialis (Morini) Q. Chen & L. Cai; Neoa. graminicola (Punith.) Q. Chen & L. Cai; Neoa. paspali (P.R. Johnst.) Q. Chen & L. Cai; Neoascochyta Q. Chen & L. Cai; Neoascochytadesmazieri (Cavara) Q. Chen & L. Cai; Neod. polemonii (Cooke) Q. Chen & L. Cai; Neod. xanthina (Sacc.) Q. Chen & L. Cai; Neodidymelliopsis Q. Chen & L. Cai; Neodidymelliopsiscannabis (Aa & Boerema) Q. Chen & L. Cai; No. arachidis-hypogaeae (V.G. Rao) Q. Chen & L. Cai; No. gossypiicola (Gruyter) Q. Chen & L. Cai; No. infossa (Ellis & Everh.) Q. Chen & L. Cai; No. quercina (Syd.) Q. Chen & L. Cai; Nothophoma Q. Chen & L. Cai; Nothophomaanigozanthi (Tassi) Q. Chen & L. Cai; Pa. putaminum (Speg.) Q. Chen & L. Cai; Pa. selaginellae (Sacc.) Q. Chen & L. Cai; Paraboeremia Q. Chen & L. Cai; Paraboeremiaadianticola (Aa & Boerema) Q. Chen & L. Cai; Phoma; Phomaneerlandica Q. Chen & L. Cai; Phomat. nebulosa (Pers.) Q. Chen & L. Cai; Phomatodes Q. Chen & L. Cai; Phomatodesaubrietiae (Moesz) Q. Chen & L. Cai; Stagonosporopsishelianthi Q. Chen & L. Cai; Taxonomy; X. asphodeli ( E. Müll.) Q. Chen & L. Cai; X. catariae (Cooke & Ellis) Q. Chen & L. Cai; X. humicola (J.C. Gilman & E.V. Abbott) Q. Chen & L. Cai; Xenodidymella Q. Chen & L. Cai; Xenodidymellaapplanata (Niessl) Q. Chen & L. Cai