Paraphoma
Morgan-Jones & J.F. White, Mycotaxon 18: 58. 1983. Fig. 41.
Fig. 41. Paraphoma spp. A–E. Disease symptoms. A, B. Crown discolouration caused by Paraphoma vinacea (ex-type BRIP 63684). C. Water-soaked and necrotic leaf lesions caused by Paraphoma chlamydocopiosa (ex-type BRIP 65168). D. Marginal leaf chlorosis caused by Paraphoma pye on pyrethrum leaf (ex-type BRIP 65169). E–O. Asexual morphs. E. Conidiomata on SNA of Paraphoma fimeti (ex-neotype CBS 170.70). F. Conidiomata of Paraphoma vinacea (ex-type BRIP 63684). G. Conidiomatal wall of Paraphoma vinacea (ex-type BRIP 63684). H. Ostiolar zone of Paraphoma vinacea (ex-type BRIP 63684). I–L. Condiogenous cells. I, J. Paraphoma dioscoreae (ex-type CBS 135100). K, L. Paraphoma fimeti (ex-neotype CBS 170.70). M, N. Conidia. M. Paraphoma dioscoreae (ex-type CBS 135100). N. Paraphoma fimeti (ex-neotype CBS 170.70). O. Chlamydospores of Paraphoma vinacea (ex-type BRIP 63684). Scale bars: F = 100 μm; G, H = 20 μm; I, K, M–O = 10 μm; I applies to I, J; K applies to K, L. Pictures B, F, G taken from Moslemi et al. (2016); C, D from Moslemi et al. (2018); I, J, M from Quaedvlieg et al. (2013).
Synonym: Phoma section Paraphoma (Morgan-Jones & J.F. White) Boerema, Stud. Mycol. 32: 7. 1990.
Classification: Dothideomycetes, Pleosporomycetidae, Pleosporales, Phaeosphaeriaceae.
Type species: Paraphoma radicina (McAlpine) Morgan-Jones & J.F. White, basionym: Pyrenochaeta radicina McAlpine. Holotype: in VPRI [Australia, Shepparton, Victoria, on roots of Prunus cerasus (Rosaceae), 21 Oct 1901, Piscott, 2064.3]. Epitype and ex-epitype strain designated by de Gruyter et al. (2010): CBS H-16560, CBS 111.79.
DNA barcodes (genus): LSU, SSU.
DNA barcodes (species): ITS, rpb2, tef1, tub2. Table 13. Fig. 42.
Table 13. DNA barcodes of accepted Paraphoma spp.
| Species | Isolates1 | GenBank accession number2 | References | |||
|---|---|---|---|---|---|---|
| ITS | tef1 | tub2 | rpb2 | |||
| Paraphoma chlamydocopiosa | BRIP 65168T | KU999072 | KU999080 | KU999084 | – | Moslemi et al. (2018) |
| Pa. chrysanthemicola | CBS 522.66NT | KF251166 | KF253124 | KF252661 | KF252174 | Quaedvlieg et al. (2013) |
| Pa. dioscoreae | CBS 135100T | KF251167 | KF253125 | KF252662 | KF252175 | Quaedvlieg et al. (2013) |
| Pa. fimeti | CBS 170.70NT | KF251170 | KF253128 | KF252665 | KF252178 | Quaedvlieg et al. (2013) |
| Pa. pye | BRIP 65169T | KU999073 | KU999081 | KU999085 | – | Moslemi et al. (2018) |
| Pa. radicina | CBS 111.79ET | KF251172 | KF253130 | KF252667 | KF252180 | Quaedvlieg et al. (2013) |
| Pa. rhaphiolepidis | CBS 142524T | KY979758 | KY979896 | KY979924 | KY979851 | Crous et al. (2017a) |
| Pa. vinacea | BRIP 63684T | KU176884 | KU176896 | KU176892 | – | Moslemi et al. (2016) |
- 1
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BRIP: Queensland Plant Pathology Herbarium, Brisbane, Australia; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands. T, ET and NT indicate ex-type, ex-epitype and ex-neotype strains, respectively.
- 2
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ITS: internal transcribed spacers and intervening 5.8S nrDNA; tef1: partial translation elongation factor 1-alpha gene; tub2: partial β-tubulin gene; rpb2: partial RNA polymerase II second largest subunit gene.
Fig. 42. Maximum likelihood PhyML combined phylogenetic tree of Paraphoma spp. inferred from ITS (680 bp), tef1 (550 bp) and tub2 (350 bp) using a GTR substitution model. Highest log likelihood -3812.4179. Bootstrap support values less than 65 % were removed. Scale bar indicated expected changes per site. The tree was rooted to Neosetophoma samarorum CBS 138.96. GenBank accession numbers are indicated in Table 13. TreeBASE: S22303.
Conidiomata pycnidial, globose to subglobose, papillate, thick-walled, pseudoparenchymatous, ostiolate, uniloculate; conidiomatal matrix white or buff, cream, yellow, brown or hyaline; setae abundant, straight or flexuous, septate, pale brown to brown, short or relatively long, stiff or hyphal-like, scattered on surface of conidiomata, or abundant around ostioles. Micropycnidia fertile or sterile, produced abundantly in some species of Paraphoma, submerged in medium. Conidiophores ampulliform, hyaline, mostly reduced to phialidic conidiogenous cells. Conidiogenous cells lageniform, monophialidic, hyaline to subhyaline. Conidia ellipsoidal to subglobose, hyaline, guttulate, aseptate in vivo and in vitro. Chlamydospores absent or present, solitary, in short or long chains or aggregated, uni- or multicellular; multicellular chlamydospores alternarioid, pseudosclerotioid, epicoccoid and botryoid depending on species. Sexual morph unknown.
Culture characteristics: Colony colour, growth and pigmentation greatly dependant on media and incubation conditions. Colonies black, brown, olivaceous, yellow, red to pink, or grey and white; slow growing; aerial mycelium flat to effuse, aerial mycelium sparsely formed, floccose to tufted, felty, woolly or compact; margins regular, smooth and sharp, or irregular, crenate and lobate.
Optimal media and cultivation conditions: CHA for colony growth and pigmentation, MEA mostly for colony pigmentation and acidified OA for both colony pigmentation and morphological identification, incubated for 1 wk in dark and 1 wk under near-ultraviolet light (13 h light, 11 h dark) at 20–22 °C to simulate colony pigmentation and sporulation.
Distribution: Temperate areas of Australia, Eurasia and North America.
Hosts: Mostly foliar pathogens of herbaceous plants, chiefly soil-borne, with wide host range including monocotyledonous plants, Asteraceae, Cupressaceae, Rosaceae and Solanaceae, occasionally saprobic.
Disease symptoms: Crown discolouration, root rot and necrotic leaf spots.
Notes: The type species of Paraphoma, Pa. radicina, clustered in a separate group outside Didymellaceae and hence was excluded from Phoma (de Gruyter et al. 2013). In a phylogenetic analysis based on LSU and SSU, Paraphoma radicina clustered in the Phaeosphaeriaceae, although other species belonged to the Cucurbitariaceae and Coniothyriaceae. Setose pycnidial conidiomata and dictyochlamydospores, which are characteristics of species of Paraphoma and Peyronellaea, can be observed in species of other phoma-like genera, such as Pyrenochaeta and Pleurophoma. Therefore, these morphological characters are not specific to these genera. In order to delineate Paraphoma, phylogenetic studies based on ITS, LSU, rpb2, tef1 and tub2 have been performed (Aveskamp et al., 2010, Moslemi et al., 2016, Moslemi et al., 2018, Crous et al., 2017a). Using ITS and LSU in combination with protein coding genes rpb2, tef1 and tub2 for precise identification of species of Paraphoma is necessary, as LSU alone is too conservative.
References: de Gruyter and Boerema, 2002, Zhang et al., 2009, Zhang et al., 2012, de Gruyter et al., 2010, de Gruyter et al., 2013 (pathogenicity, phylogeny and distribution); Boerema et al. 2004 (morphology, pathogenicity, media and incubation conditions); Aveskamp et al., 2009, Aveskamp et al., 2010 (morphology, phylogeny and key of all Paraphoma spp.); Hay et al. 2015 (hosts).
Authors: A. Moslemi, P.W.J. Taylor & P.W. Crous