Nothophoma Qian Chen & L. Cai, Stud. Mycol. 82: 212 (2015)


Nothophoma was introduced by Chen et al. (2015b) by transferring five Phoma species. Species are saprobes and pathogens. In addition, to the phytopathogens, N. gossypiicola has been isolated from clinical samples of humans in the respiratory secretion of a patient with pneumonia and a human bronchial wash sample (Valenzuela-Lopez et al. 2018). Chethana et al. (2019) showed that the comparative pathogenicity of Nothophoma species is low when compared to other opportunistic pathogens. Some species grow on other fungi or occur in soil (Boerema et al. 2004, Aveskamp et al. 2009, 2010, Chen et al. 2015b;). Some Nothophoma species might be host-specific to a single plant genus or family (Aveskamp et al. 2010; Chen et al. 2015b). However, there is no study of host-specificity in Didymellaceae. Abdel-Wahab et al. (2017) identified 55 bioactive compounds from an endophyte, N. multilocularis. Of these, ten compounds showed strong antimicrobial activity in combination.

Classification Ascomycota, Pezizomycotina, Dothideomycetes, Pleosporomycetidae, Pleosporales, Didymellaceae

Type species Nothophoma infossa (Ellis & Everh.) Qian Chen & L. Cai

Distribution Argentina, China, Italy, India, Korea, Netherlands, Spain, Tunisia, Ukraine, United States

Disease symptoms brown spot of fruits, leaf spots, shoot canker, stem cankers

Leaf spot produced by Nothophoma anigozanthi is elliptical to circular and black. Nothophoma pruni and N. quercina develop small, dark red or purple pinpoint lesions (Chethana et al. 2019). Liu et al. (2018b) identified N. quercina infection on ornamental crab-apple. Symptoms on the trunk appear as warts, the periderm around warts can become cracked, and the bark is roughened with a scaly periderm. During dry weather, these cankers expand and coalesce (Liu et al. 2018b; Fig 1). Nothophoma quercina develops shoot necrosis, stem browning, and wilted leaves on Chaenomeles sinensis (Yun and Oh 2016). In Tunisia, shoot blights caused by N. quercina were observed with diffuse cankers with gummosis on buds (Triki et al. 2019).

Hosts— Has a wide range of hosts including Anigozanthos flavidus, Anigozanthus maugleisii, Arachis hypogaea, Chaenomeles sinensis, Gossypium sp., Fraxinu spennsylvanica, Malus micromalus, Microsphaera alphitoides, Olea europaea, Phellodendrona murense, Pistacia vera, Prunu savium, Prunus dulcis, Spiraea salicifolia, Quercus sp. and Ziziphus jujube (Babaahmadi et al. 2018; Chen et al 2015b, 2017; Chethana et al. 2019; Jianyu et al. 2016; Liu et al. 2018b; Moral et al. 2017, 2018; Soleimani et al. 2018; Triki et al. 2019; Valenzuela-Lopez et al. 2018; Yun and Oh 2016; Zhang et al. 2020).

Morphological based identification and diversity

This genus was introduced by Chen et al. (2015b) based on molecular data to delineate a more natural classification for the AscochytaDidymellaPhoma species complex (Chen et al. 2015b; Fig. 23). Species produce elongate, barrel-shaped, olivaceous brown chlamydospores in chains (Chen et al. 2015b). However, there is little morphological variation among species (Valenzuela-Lopez et al. 2018).

Fig. 1 Nothophoma quercina on Malus micromalus aMalus micromalus (Crab-Apple tree).b Canker on the trunk. c, d appearance of conidiomata on trunk. e longitudinal section through conidiomata. f cross-section of conidiomata g, h conidiogenous cells. i, j conidia. k upper view on PDA. l reverse view on PDA. Scale bars: d=1000 μm e–f = 50μm g–j 10 μm.

Molecular based identification and diversity

Species identification is based on multi-locus sequence phylogeny. Phylogenetic analyses of combined LSU, ITS, tub2 and rpb2 sequence data resulted in several new species being added to this genus by Chen et al. (2015b), Abdel-Wahab et al. (2017), Valenzuela-Lopez et al. (2018), Chethana et al. (2019), Marin-Felix et al. (2019) and Zhang et al. (2020). Here we provide an updated phylogenetic tree for this genus (Fig. 2).

Recommended genetic markers (genus level)LSU, ITS

Recommended genetic markers (species level) – tub2, rpb2

Since the colony morphology and other morphological features in Didymellaceae often overlap, initial species identification is recommended with LSU and ITS sequence data using all type species in Didymellaceae. Once the genus is identified as Nothophoma, the phylogenetic analysis could be done with LSU, ITS, tub2, and rpb2 sequence data.

Accepted number of species There are 12 species in Index Fungorum (2020) with DNA sequence data (Table 1).

References Chen et al. 2015b, Abdel-Wahab et al. 2017, Valenzuela-Lopez et al. 2018, Chethana et al. 2019, Marin-Felix et al. 2019, Zhang et al. 2020 (morphology and phylogeny)


Table 1 DNA barcodes available for Nothophoma. Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with #.

Species Isolate LSU ITS tub2 RPB2
Nothophoma anigozanthi CBS 381.91* GU238039 GU237852 GU237580 KT389655
N. arachidis-hypogaeae CBS 125.93 GU238043 GU237771 GU237583 KT389656
N. brennandiae CBS 145912* MN823430 MN823579 MN824753 MN824604
  JW 1066 MN823429 MN823578 MN824752 MN824603
N. gossypiicola CBS 377.67 GU238079 GU237845 GU237611 KT389658
  UTHSC:DI16-294 LN907437 LT592943 LT593012 LT593082
N. infossa CBS 123395 * GU238089 FJ427025 FJ427135 KT389659
N. macrospora CBS 140674 * LN880537 LN880536 LN880539 LT593073
N. multilocularis AUMC-12003* KY996744
N. pruni# MFLUCC 18–1600 * MH827028 MH827007 MH853671 MH853664
  MFLUCC18–1601 MH827026 MH827005 MH853669 MH853662
N. quercina# CBS 633.92 EU754127 GU237900 GU237609 KT389657
  UTHSC:DI16-270 LN907413 LT592929 LT592998 LT593067
N. raii MCC 1082 * MF664467 MF664468
N. spiraeae CFCC 53928* MN737828 MN737833 MN879295 MN879292
  CFCC 53929 MN737829 MN737834 MN879296 MN879293
N. variabilis UTHSC: DI16-285* LN907428 LT592939 LT593008 LT593078

Fig. 2 Phylogram generated from maximum likelihood analysis based on combined LSU, ITS, tub2 and rpb2 sequence data of Nothophoma species. Related sequences were obtained from GenBank. Seventeen strains are included in the combined sequence analyses. Phoma herbarum (CBS 615.75) and Vacuiphoma bulgarica (CBS 357.84) was used as the outgroup taxa. The best scoring RAxML tree with a final likelihood value of -5537.646741is presented. The matrix had 284 distinct alignment patterns, with 12.23% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.238395, C = 0.241637, G = 0.276596, T = 0.243371; substitution rates AC = 0.975188, AG = 4.004775, AT = 1.500008, CG = 0.519461, CT = 10.843965, GT = 1.000000; gamma distribution shape parameter a = 1.764918. ML bootstrap support value ≥50% and BYPP ≥0.95 are shown respectively near the nodes. Ex-type strains are in bold.

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