The phoma-like dilemma

L W Hou; J Z Groenewald; L H Pfenning; O Yarden; P W Crous; L Cai

doi:10.1016/j.simyco.2020.05.001

The phoma-like dilemma

Stud Mycol. 2020 May 21:96:309-396. doi: 10.1016/j.simyco.2020.05.001. eCollection 2020 Jun.

Authors

L W Hou^{1

2}, J Z Groenewald³, L H Pfenning⁴, O Yarden⁵, P W Crous^{3

6

7

8}, L Cai^{1

2}

Affiliations

¹ State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
² University of Chinese Academy of Sciences, Beijing, 100049, China.
³ Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands.
⁴ Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, MG 37200-000, Brazil.
⁵ Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, 76100, Israel.
⁶ Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
⁷ Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.
⁸ Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.

Abstract

Species of Didymellaceae have a cosmopolitan distribution and are geographically widespread, occurring in diverse ecosystems. The family includes several important plant pathogenic fungi associated with fruit, leaf, stem and root diseases on a wide variety of hosts, as well as endophytic, saprobic and clinically relevant species. The Didymellaceae was recently revised based on morphological and phylogenetic analyses of ex-type strains subjected to DNA sequencing of partial gene data of the LSU, ITS, rpb2 and tub2 loci. Several poly- and paraphyletic genera, including Ascochyta, Didymella and Phoma were redefined, along with the introduction of new genera. In the present study, a global collection of 1 124 Didymellaceae strains from 92 countries, 121 plant families and 55 other substrates, including air, coral, human tissues, house dust, fungi, insects, soil, and water were examined via multi-locus phylogenetic analyses and detailed morphological comparisons, representing the broadest sampling of Didymellaceae to date. Among these, 97 isolates representing seven new genera, 40 new species and 21 new combinations were newly introduced in Didymellaceae. In addition, six epitypes and six neotypes were designated to stabilise the taxonomy and use of older names. A robust, multi-locus reference phylogenetic tree of Didymellaceae was generated. In addition, rpb2 was revealed as the most effective locus for the identification of Didymellaceae at species level, and is proposed as a secondary DNA marker for the family.

Keywords: Al. anatii L.W. Hou & O. Yarden; Allophomaalba L.W. Hou, Pfenning, L. Cai & Crous; Amphisphaeria vincetoxici De Not.; As. koolunga (J.A. Davidson et al.) L.W. Hou, L. Cai & Crous; Ascochyta ferulae Pat.; Ascochyta nobilis Kabát & Bubák; Ascochytaastragalina (Rehm ex Sacc.) L.W. Hou, L. Cai & Crous; Ascochytapilosella L.W. Hou, L. Cai & Crous; Calophomaparvula L.W. Hou, L. Cai & Crous; Calophomavincetoxici (De Not.) L.W. Hou, L. Cai & Crous; Chaetasbolisiaargentina L.W. Hou, L. Cai & Crous; Chaetasbolisiaeupatorii (Died.) L.W. Hou, L. Cai & Crous; Did. guttulata L.W. Hou, L. Cai & Crous; Did. indica L.W. Hou, L. Cai & Crous; Did. mitis L.W. Hou, L. Cai & Crous; Did. prolaticolla L.W. Hou, L. Cai & Crous; Did. prosopidis (Crous & A.R. Wood) L.W. Hou, L. Cai & Crous; Did. subglobispora L.W. Hou, L. Cai & Crous; Did. subrosea L.W. Hou, L. Cai & Crous; Did. variabilis L.W. Hou, L. Cai & Crous; Didymellaaloeicola L.W. Hou, L. Cai & Crous; Didymellacombreti (Crous) L.W. Hou, L. Cai & Crous; Dimorphoma L.W. Hou, L. Cai & Crous; Dimorphomasaxea (Aveskamp et al.) L.W. Hou, L. Cai & Crous; Ectodidymella L.W. Hou, L. Cai & Crous; Ectodidymellanigrificans (P. Karst.) L.W. Hou, L. Cai & Crous; Ectophomainsulana (Mont.) L.W. Hou, L. Cai & Crous; Ep. dickmanii L.W. Hou & O. Yarden; Ep. longiostiolatum L.W. Hou, L. Cai & Crous; Ep. multiceps L.W. Hou, L. Cai & Crous; Ep. oryzae Ito & Iwadare; Ep. polychromum L.W. Hou, L. Cai & Crous; Ep. purpurascens Ehrenb.; Ep. variabile L.W. Hou, L. Cai & Crous; Epicoccum mezzettii Goid.; Epicoccum oryzae S. Ito & Iwadare; Epicoccumbrahmansense L.W. Hou, L. Cai & Crous; Epicoccumtobaicum (Szilv.) L.W. Hou, L. Cai & Crous; Heterophoma verbasci-densiflori L.W. Hou, L. Cai & Crous; Le. sisyrinchiicola L.W. Hou, L. Cai & Crous; Leptosphaerulinaobtusispora L.W. Hou, L. Cai & Crous; Lo. vitalbae (Briard & Har.) L.W. Hou, L. Cai & Crous; Longididymella L.W. Hou, L. Cai & Crous; Longididymellaclematidis (Woudenb. et al.) L.W. Hou, L. Cai & Crous; Ma. terrestris L.W. Hou, L. Cai & Crous; Macroascochyta L.W. Hou, L. Cai & Crous; Macroascochytagrandis L.W. Hou, L. Cai & Crous; Macroventuriaangustispora L.W. Hou, L. Cai & Crous; Mi. taxicola L.W. Hou, L. Cai & Crous; Mi. viridis L.W. Hou, L. Cai & Crous; Microsphaeropsisfusca L.W. Hou, L. Cai & Crous; Multi-locus phylogeny; Neoa. humicola L.W. Hou, L. Cai & Crous; Neoa. longispora L.W. Hou, L. Cai & Crous; Neoa. mortariensis L.W. Hou, L. Cai & Crous; Neoascochytafusiformis L.W. Hou, L. Cai & Crous; Neodidymelliopsistiliae L.W. Hou, L. Cai & Crous; New taxa; No. eucalyptigena (Crous) L.W. Hou, L. Cai & Crous; No. prosopidis (Crous & A.R. Wood) L.W. Hou, L. Cai & Crous; Nothophoma nullicana L.W. Hou, L. Cai & Crous; Nothophomaacaciae (Crous) L.W. Hou, L. Cai & Crous; Nothophomainfuscata L.W. Hou, L. Cai & Crous; Paramicrosphaeropsis L.W. Hou, L. Cai & Crous; Paramicrosphaeropsisellipsoidea L.W. Hou, L. Cai & Crous; Phoma; Phoma eupatorii Died; Phoma eupatorii Died.; Phoma laurina Thüm., Phoma nemophilae Neerg.; Phomatodespilosa L.W. Hou, L. Cai & Crous; Phyllosticta acetosellae A.L. Sm. & Ramsb.; Phyllosticta arachidis-hypogaeae V.G. Rao; Phyllosticta insulana Mont; Phyllosticta verbascicola Ellis & Kellerm.; Pleosphaerulina briosiana Pollacci; Pseudopeyronellaea L.W. Hou, L. Cai & Crous; Pseudopeyronellaeaeucalypti (Crous & M.J. Wingf.) L.W. Hou, L. Cai & Crous; R. humicola L.W. Hou, L. Cai & Crous; Remotididymellabrunnea L.W. Hou, L. Cai & Crous; Remotididymellacapsici (Bond.-Mont.) L.W. Hou, L. Cai & Crous; Sclerotiophoma L.W. Hou, L. Cai & Crous; Sclerotiophomaversabilis (Boerema et al.) L.W. Hou, L. Cai & Crous; St. sambucella L.W. Hou, L. Cai & Crous; Stagonosporopsiscucumeris L.W. Hou, L. Cai & Crous; Stagonosporopsisnemophilae (Neerg). L.W. Hou, L. Cai & Crous; Taxonomy; Toruloidea tobaica Szilv; Va. laurina (Thüm.) L.W. Hou, L. Cai & Crous; Vacuiphomaferulae (Pat.) L.W. Hou, L. Cai & Crous; Xenodidymellaglycyrrhizicola L.W. Hou, L. Cai & Crous; rpb2.