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. 2021 Mar 1;9:e63643. doi: 10.3897/BDJ.9.e63643

Allophoma species (Pleosporales: Didymellaceae) associated with Thunbergia grandiflora in Guangxi Province, China

Jun Yuan 1, Xiang-Yu Zeng 1, Kun Geng 2, Nalin N Wijayawardene 3, Jayarama D Bhat 4, Shi-Ping Wu 5, Yong Wang 1,✉, Zai-Fu Yang 1
PMCID: PMC7940324  PMID: 33692649

Abstract

Background

Thunbergia grandiflora belongs to the family Acanthaceae and is a widely distributed dicotyledonous plant in tropical and subtropical regions. Three isolates of Allophoma (Dothideomycetes, Pleosporales, Didymellaceae) were collected from leaves of T. grandiflora in Guangxi Province, China.

New information

Phylogenetic analyses of a combined ITS–LSU–rpb2–tub2 dataset indicate that one of our three strains represents an undescribed species with close affinity to A. minor and the other two strains clustered amongst other isolates of A. pterospermicola. Evidence from morphology and sequence analysis indicates that GUCC 2070.7 is a new species that we introduce here as A. thunbergiae. This is the first report about taxa of Allophoma from this host plant.

Keywords: one new species, Didymellaceae , phylogeny, taxonomy

Introduction

Didymellaceae was established by De Gruyter et al. (2009) with Didymella as the type genus. It is the largest family in the Pleosporales and accommodates more than 5400 taxon names (Crous et al. 2004), including saprobic, endophytic and pathogenic species (Aveskamp et al. 2008, Aveskamp et al. 2010, Marin-Felix et al. 2017). A great part of Didymellaceae species are reported as plant pathogens, which cause severe economic losses to many crops (Aveskamp et al. 2008). Recently, Didymellaceae was revised, based on morphological and phylogenetic analyses of ex-type sequences of LSU, ITS, rpb2 and tub2 loci, resulting in 19 genera (Chen et al. 2015, Chen et al. 2017), Currently, 37 genera are accepted (Wijayawardene et al. 2017, Wijayawardene et al. 2020, Valenzuela-Lopez et al. 2018, Hou et al. 2020a, Hou et al. 2020b, Phukhamsakda et al. 2020).

Allophoma is presently accepted with 14 species (Hongsanan et al. 2020, Hou et al. 2020a, Hyde et al. 2020, Wijayawardene et al. 2020) and two of them were firstly obtained from Guizhou and Guangxi Provinces, China (Chen et al. 2017, Marin-Felix et al. 2019). The genus includes several important plant-pathogenic taxa, for example, Allophoma labilis (basionym: Phoma labilis), which often cause leaf necrosis, canker and stem lesions or stem rot, resulting in a negative effect on the health of plants (Zimowska 2011, Garibaldi et al. 2012, Nagarjun and Suryanarayana 2016, O'Neill and Mayne 2016, Babaahmadi et al. 2018,Jayasiri et al. 2019). Allophoma is characterised by superficial or immersed pycnidial conidiomata with ostioles, a 2−5-layered pseudo-parenchymatous wall, phialidic conidiogenous cells and aseptate variously-shaped, mostly guttulate conidia. The size of the pycnidia, conidiogenous cells and conidia are used to distinguish amongst different species in Allophoma (Chen et al. 2015).

In recent years, most species of fungi have been described from Asia, mostly China (Cheek et al. 2020). Our research group investigates the fungi on medicinal plants in south-western China, which has, thus far, resulted in the discovery of several new taxa (Long et al. 2019, Zhang et al. 2020a, Zhang et al. 2020b, An et al. 2021). Here, we studied diseased leaves of Thunbergia grandiflora collected from the Medicinal Botanical Garden in Nanning City, Guangxi Province, China. Following isolation, purification, morphological examination and phylogenetic analyses, a new species and one known species were discovered.

Materials and methods

Isolation and morphological study

The samples were collected in 2017 at the Medicinal Botanical Garden, Nanning, Guangxi, China. Single spore isolates were obtained on oatmeal agar (OA), malt extract agar (MEA) and potato dextrose agar (PDA), followed by incubation at 25 °C. Colony diameters were measured after 1 week (Boerema et al. 2004). The colour of colonies of inoculated Petri dishes was determined following Rayner (1970). Morphological structures were examined and photographed using a Nikon Eclipse 80i microscope. Micro-morphological descriptions and measurements of mature conidiomata, conidia and conidiogenous cells on OA or MEA and PDA cultures were based on Aveskamp et al. (2010). The holotype specimen is deposited at the Herbarium of the Department of Plant Pathology, Agricultural College, Guizhou University (HGUP). An ex-type culture of the new taxon is deposited at the Culture Collection of the Department of Plant Pathology, Agriculture College, Guizhou University (GUCC) (Table 1).

Table 1.

Sequences that were used for phylogenetic analysis. The accession numbers in bold are those generated in this study. Ex-type strains are marked by an asterisk (*).

Species Strain number GenBank accession numbers
LSU ITS rpb2 tub2
Allophoma alba CBS 120422 MN943671 MN973469 MT018044 MT005568
A. anatii CBS 124673 MN943674 MN973472 MT018048 MT005571
A. cylindrispora CBS 142453* LN907376 LT592920 LT593058 LT592989
A. hayatii CBS 142859 KY684814 KY684812 MF095108 KY684816
A. hayatii CBS 142860 KY684815 KY684813 MF095109 KY684817
A. labilis CBS 124.93 GU238091 GU237765 KT389552 GU237619
A. minor CBS 325.82* GU238107 GU237831 KT389553 GU237632
A. nicaraguensis CBS 506.91* GU238058 GU237876 KT389551 GU237596
A. oligotrophica CBS 497.91 GU238059 GU237870 GU237597 LT623247
A. oligotrophica CGMCC 3.18114* KY742194 KY742040 KY742128 KY742282
A. oligotrophica CGMCC 3.18115 KY742195 KY742041 KY742129 KY742283
A. oligotrophica CGMCC 3.18116 KY742196 KY742042 KY742130 KY742284
A. piperis CBS 268.93* GU238129 GU237816 KT389554 GU237644
A. piperis CBS 108.93 GU238130 GU237921 KT389555 GU237645
A. pterospermicola CGMCC 3.19245* MK088580 MK088573 MK088587 MK088594
A. pterospermicola LC12181 MK088576 MK088569 MK088583 MK088590
A. pterospermicola LC12182 MK088577 MK088570 MK088584 MK088591
A. pterospermicola LC12183 MK088578 MK088571 MK088585 MK088592
A. pterospermicola LC12184 MK088579 MK088572 MK088586 MK088593
A. pterospermicola GUCC2070.6 MW040200 MW036297 MW116818 MW116822
A. pterospermicola GUCC2070.3 MW040199 MW036296 MW116817 MW116821
A. siamensis MFLU 17-2281 MK347959 MK347742 MK434912 MK412867
A. thunbergiae GUCC2070.7 MW040201 MW036298 MW116819 MW116823
A. tropica CBS 436.75* GU238149 GU237864 KT389556 GU237663
A. zantedeschiae CBS 131.93 GU238159 FJ427084 KT389557 FJ427188
A. zantedeschiae CBS 229.32 KT389690 KT389473 KT389558 KT389767
A. zantedeschiae ICMP 16850 KY742197 KY742043 KY742131 KY742285
Stagonosporopsis loticola CBS 562.81* GU238192 GU237890 KT389684 GU237697
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DNA isolation, PCR and sequencing

Fungal mycelia were scraped off the surface of the pure culture plate with a sterile scalpel. Total genomic DNA was extracted using the A BIOMIGA Fungus Genomic DNA Extraction Kit (GD2416, BIOMIGA, San Diego, California, USA). Four loci of each fungal strains were amplified, including the internal transcribed spacer (ITS) region with primers V9G (De Hoog and Van den Ended 1998) and ITS4 (White et al. 1990); the large subunit (LSU) of the ribosomal RNA gene with primers LR0R (Hopple 1994), LR5 and LR7 (Vilgalys and Hester 1990); the second-largest subunit of the RNA polymerase II (rpb2) wih primers RPB2-5F2 (Sung et al. 2007) and fRPB2-7cR (Liu et al. 1999); and β-tubulin (tub2) with primers Btub2Fd and Btub4Rd (Woudenberg et al. 2009). DNA amplifications were performed in 25-μl reaction volumes, containing 2.5 μl 10 × PCR buffer, 1 μl of each primer (10 μM), 1 μl template DNA, 0.25 μlTaq DNA polymerase (Promega, Madison, WI, USA) and 18.5 μl ddH2O. The PCR cycling conditions for ITS were as follows: initial denaturation at 95°C for 5 min; then 35 cycles of denaturation at 95°C for 30 s, annealing at 52°C for 45 s and extension at 72°C for 90 s; and final extension at 72°C for 10 min. For LSU: initial denaturation at 98°C for 3 min; then 35 cycles of denaturation at 98°C for 30 s, annealing at 45°C for 27 s and extension at 72°C for 30 s; and final extension at 72°C for 10 min. For rpb2: initial denaturation at 95°C for 5 min; then 40 cycles of denaturation at 95°C for 1 min, annealing at 55°C for 2 min and extension at 72°C for 90 s; and final extension at 72°C for 10 min. For tub2: initial denaturation at 94°C for 3 min; then 35 cycles of denaturation at 94°C for 1 min, annealing at 58°C for 45 s and extension at 72°C for 1 min; and final extension at 72°C for 10 min. The amplification products were sent to SinoGenoMax (Beijing) for sequencing. The newly-generated DNA sequences were submitted to GenBank (accession numbers in Table 1). The DNA base differences on four loci amongst our strains and ex-type or representative strains of relative Allophoma taxa are shown in Table 2.

Table 2.

DNA base differences amongst our strains and related species in four gene regions.

Species Strain number ITS (1-494bp) rpb2 (495-1090bp) tub2 (1091-1424bp) LSU (1425-2729bp)
Allophoma thunbergiae GUCC 2070.7 0 0 0 0
A. piperis CBS 268.93 * 21 39 26 0
A. minor CBS 325.82* 6 1 9 0
A. pterospermicola GUCC 2070.3 0 0 0 0
A. pterospermicola GUCC 2070.6 5 0 1 4
A. pterospermicola CGMCC 3.19245* 1 0 1 3
A. siamensis MFLU 17-2281 4 55 1 6
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Sequence alignment and phylogenetic analyses

The related DNA sequences for phylogenetic analyses in this study were downloaded from GenBank (Table 1). Amongst them, Stagonosporopsis loticola (CBS 562.81) is regarded as outgroup taxon. Alignments for four individual loci were constructed (ITS, rpb2, tub2 and LSU) in MAFFT v7.307 online version (Katoh and Standley 2016) and were manually edited in MEGA v. 6.0 when necessary (Tamura et al. 2013). The concatenated aligned dataset and each locus were analyzed separately using Maximum Likelihood (ML), Bayesian Inference (BI) and Maximum Parsimony (MP).The best fit substitution model for each gene was tested from eleven substitution schemes by using ‘jModelTest2 on XSEDE’ tool (Darriba et al. 2012) at the CIPRES web portal (Miller et al. 2010), and determined by the Bayesian information criterion (BIC).ML analysis was performed using RAxML-HPC2 v. 8.2.12 (Stamatakis 2014) as implemented on the CIPRES Science Gateway, with the GTR+G+I model and 1,000 rapid bootstrap (BS) replicates for four genes. For BI analysis, the best substitution model for each partition was determined with the program MrModeltest 2.2 (Nylander 2004) to be GTR+G+I. BI analysis was performed using MrBayes v.3.2.6 (Ronquist et al. 2012) as implemented on the Cipres portal (Miller et al. 2010). Parameters and tree samples were summarized with a burn-in fraction of 0.25, which were checked against the log likelihood by sampled generation plot. MP analysis was performed in PAUP v. 4.0b10 (Swofford 2002) using the heuristic search option with 1,000 random taxa additions and tree bisection and reconnection (TBR) as the branch-swapping algorithm. The maxtrees were set as 5000 to build up the phylogenetic tree. The Tree Length (TL), Consistency Indices (CI), Retention Indices (RI), Rescaled Consistency Indices (RC) and Homoplasy Index (HI) were calculated for each tree generated.

Taxon treatments

Allophoma thunbergiae

Jun Yuan & Yong Wang bis sp. nov.

12E84C9E-A66C-5636-946A-8241BBD00913

558130

Materials

  1. Type status: Holotype. Occurrence: recordedBy: Jun Yuan; occurrenceID: GUCC 2070.7; Taxon: scientificName: Allophoma thunbergiae; order: Pleosporales; family: Didymellaceae; genus: Allophoma; Location: country: China; stateProvince: GuangXi; locality: Nanning City, Guangxi Medicinal Botanical Garden; verbatimCoordinates: 22°51’N, 108°19’E; Identification: identifiedBy: Jun Yuan; dateIdentified: 2020; Record Level: collectionID: HGUP 2070.7

Description

Pathogenic on the leaf spot of Thunbergia grandiflora. Lesions initially on the upper leaf surface, scattered, distinct, irregular, the maximum length of the spot more than 10-15 mm, the edge of the spots yellow, the centre of necrotic section brown, on the lower leaf surface similar. Sexual morph: Undetermined. Asexual morph (Fig. 1): Coelomycetous. Conidiomata pycnidial, mostly solitary or aggregated, subglobose to irregular, dark brown, glabrous, covered with some hyphal outgrowths, produced on the agar surface or (semi-)immersed, ostiolate, (39−)44−200 × (48−)49−230 μm (x̄ = 108.9 × 138.9 μm, n = 20). Ostioles 1−3, with a short neck, slightly papillate or sometimes non-papillate. Pycnidial wall pseudoparenchymatous, composed of oblong to isodiametric cells, 3−4 layered, 14−32 μm thick (x̄ = 20.8 μm, n = 10). Conidiogenous cells phialidic, hyaline, smooth, ampulliform to doliiform, 4.5−7 × 4−5 μm (x̄ = 4.9 × 4.6 μm, n = 10), with a distinct periclinal thickening. Conidia oblong to cylindrical, slightly obovoid, smooth and thin-walled, hyaline, aseptate, 3−5 × 1.5−2.5 μm (x̄ = 3.6 × 2.2 μm, n = 20), with two minutes guttules. Conidial exudates not recorded.

Figure 1.

Figure 1.

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Allophoma thunbergiae (GUCC2070.7) a. Leaf symptoms on the host; b, c. Pycnidia forming on PDA; d, e. Colony on PDA (front and reverse); f, g. Colony on MEA (front and reverse); h, i. Colony on OA (front and reverse); j, k. Section of pycnidium; l. Section of pycnidial wall; m, n. Conidiogenous cells; o. Conidia. Scale bars: b, c = 500 μm; j = 100 μm; k = 50 μm; l = 20 μm; m−o = 5 μm.

Culture characteristics: Colonies on PDA, 46−57 mm diameter after 1 week, irregular at margin, aerial mycelia floccose, grey with a white margin, brown near the centre; reverse pale brown, with a white margin. Colonies on MEA 44−47 mm diameter after 1 week, regular at margin, covered by brown, dense aerial mycelia, yellow near the centre; reverse greyish-brown. Colonies on OA, 41−46 mm diameter after 1 week, irregular at margin, covered by white aerial mycelia sparse, brownish, reverse buff to yellowish-olivaceous.

Etymology

In reference to the host (Thunbergia grandiflora), from which the fungus was isolated.

Allophoma pterospermicola

Qian Chen & L. Cai, Stud. Mycol. 94: 4 (2019)

D929DD22-05E0-57B7-871B-E45F483E537B

828313

Materials

  1. Type status: Other material. Occurrence: recordedBy: Jun Yuan; occurrenceID: GUCC 2070.3 and GUCC 2070.6; Taxon: scientificName: Allophoma pterospermicola; order: Pleosporales; family: Didymellaceae; genus: Allophoma; Location: country: China; stateProvince: GuangXi; locality: Nanning City, Guangxi Medicinal Botanical Garden; verbatimCoordinates: 22°51’N, 108°19’E; Identification: identifiedBy: Jun Yuan; dateIdentified: 2020; Record Level: collectionID: HGUP 2070.3 and HGUP 2070.6

Description

Pathogenic on the leaf spot of Thunbergia grandiflora. Lesions initially on the upper leaf surface, scattered, distinct, irregular, the maximum length of the spot more than 10-13 mm, the edge of the spots yellow, the necrotic section brown at the later stage connected to form the dead leaves, on the lower leaf surface similar. Sexual morph: Undetermined. Asexual morph (Fig. 2): Coelomycetous. Conidiomata pycnidial, mostly aggregated and those aggregates are solitary, scattered, globose, subglobose or sometimes irregular, dark brown, glabrous, covered with some hyphal outgrowths, produced on the toothpick surface, ostiolate, (42−)52−208 × (25−)63−147 μm (x̄ = 108.1 × 99.3 μm, n = 20). Ostiole single, with a short neck, slightly papillate. Pycnidial wall pseudoparenchymatous, composed of oblong to isodiametric cells, 3−6 layers, 18−36 μm thick (x̄ = 23.6 μm, n = 10). Conidiogenous cells phialidic, hyaline, smooth, ampulliform to doliiform, 3.5−6 × 3.5−4 μm (x̄ = 3.8 × 4.3 μm, n = 10). Conidia ellipsoidal to oblong, incidentally slightly obovoid, smooth and thin-walled, hyaline, aseptate, 2.5−4 × 1.5−2.5 μm (x̄ = 3.5 × 2.5 μm, n = 20), with 2 distinct polar guttules. Conidial exudates not recorded.

Figure 2.

Figure 2.

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Allophoma pterospermicola (GUCC2070.3) a, b. Colony on PDA (front and reverse); c, d. Colony on MEA (front and reverse); e, f. Colony on OA (front and reverse); g. Leaf symptoms on the host; h-j. Pycnidia forming on the toothpick; k. Pycnidium; l. section of pycnidium; m. Section of pycnidial wall; n, o. Conidiogenous cells; p. Conidia. Scale bars: h, i = 500 μm; j = 100 μm; k = 50 μm; l, m = 20 μm; n−p = 5 μm.

Culture characteristics: Colonies on PDA, 46−50 mm diameter after 1 week, regular at margin, densely covered by floccose aerial mycelia, grey, with a white concentric ring near the margin; reverse pale black, with a white concentric ring near the margin. Colonies on MEA, 52−58 mm diameter after 1 week, regular at margin, dull green, aerial mycelia floccose, aerial mycelia sparsely, grey near the centre; reverse changing towards margin from the centre greyish-brown to brown. Colonies on OA 34−47 mm diameter after 1 week, irregular at margin, covered by floccose aerial mycelia, mycelia sparse in some furrowed zone, reverse buff to pale olivaceous.

Analysis

Phylogenetic analyses (Fig. 3

Figure 3.

Figure 3.

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Phylogenetic tree inferred from a Maximum Parsimonious analysis, based on a concatenated alignment of ITS, rpb2, tub2 and LSU sequences. ML bootstrap support values (MLBS) ≥ 70, BI posterior probabilities (BIPP) ≥ 0.90, and MP boostrap support values (MPBS) ≥ 70 are given at the nodes. The tree was rooted to Stagonosporopsis loticola (CBS 562.81). Newly-generated isolates are in bold. Ex-type strains are marked by an asterisk (*).

Discussion

Phoma sensu lato was previously a large genus with phoma-like species (De Gruyter et al. 2012), but was recently characterised using molecular data, resulting in many species that were transferred to new genera, such as Allophoma (Chen et al. 2015). In this study, our isolates from Thunbergia (GUCC 2070.3, GUCC 2070.6 and GUCC 2070.7) represent species of Allophoma (Didymellaceae). One of these isolates, GUCC 2070.7, was retrieved close to A. minor in our phylogenetic tree (Fig. 3). In Table 3, we provide a comprehensive comparison of pycnidia, conidiogenous cells and conidia, which indicates that strain GUCC 2070.7 has smaller pycnidia (39−200 × 48−230 μm vs. 150−280 × 150−220 μm) and larger conidiogenous cells (4.5−7 × 4−5 μm vs. 4−5.5 × 3−4.5 μm) than A. minor. The phylogenetic analyses and comparison of DNA base pairs confirm that strain GUCC 2070.7 is different from A. minor sensu Jeewon and Hyde (2016). In summary, strain GUCC 2070.7 represented an undescribed species, A. thunbergiae, whereas strains GUCC 2070.3 and GUCC 2070.6 are A. pterospermicola, based on phylogenetic analyses and morphological studies (Chen et al. 2017, Fig. 3, Table 2). Thunbergia grandiflora, native to China, is here reported as a host for Allophoma species for the first time.

Table 3.

The pycnidia, conidiogenous cells, and conidia morphology of the new species compared to known species of Allophoma.

Species Pycnidia Conidiogenous cells Conidia References
Shape Size (μm) Size (μm) Shape Size (μm)
Allophoma alba (sub-)globose to ellipsoidal, whitish at onset 205−635 × 195−510 3.5−6.5 × 4.5−9 oblong, with both ends rounded, hyaline, smooth and thin-walled, aseptate 3−4.5 × 1.5−2.3 Hou et al. (2020b)
A. anatii (sub-)globose to ellipsoidal 130−400 × 120−370 5−7 × 5.5−9 oblong with both ends rounded or ovoid, smooth and thin-walled, hyaline, aseptate 3.5−5.5 × 2−3 Hou et al. (2020b)
A. cylindrispora glabrous, ovoid 120−210 × 90−140 3.5−4 × 4.5−5 aseptate, hyaline, smooth and thin-walled, cylindrical 3−4 × 2 Valenzuela-Lopez et al. (2018)
A. hayatii (sub-)globose with 1−2 narrow and long necks 125 × 102 - oblong to ellipsoidal 3.3−8 × 2.2−3.3 Babaahmadi et al. (2018)
A. labilis globose 250 × 70 5−7 × 4−8 oblong to ellipsoidal 4−6.5 × 2–3 De Gruyter and Noordeloos (1992) Boerema et al. 2004
A. minor globose to broadly ellipsoidal 150−280 × 150−220 4−5.5 × 3−4.5 ellipsoidal to ovoid or slightly allantoid 3.5−4.5 × 1.8−2.5 Aveskamp et al. (2010)
A. nicaraguensis globose to flask-shaped 30−150 × 28−120 3−4.5 × 3.5−4.5 ellipsoidal to oblong 2.5−4 × 1.5−2.5 Chen et al. (2015)
A. oligotrophica globose to subglobose 50−440 × 145−420 4.5−7 × 3.5−6.5 oblong to cylindrical 3−4.5 × 1.5−2.5 Chen et al. (2017)
A. piperis subglobose 115−245 × 85−230 2.5−3.5 × 2−3 ellipsoidal to ovoid or slightly allantoid 3.5−5.5 × 1.5−2.5 Chen et al. (2015)
A. pterospermicola globose to subglobose, brown, glabrous 60−330 × 67−280 6−10 × 3−6 oval to oblong, occasionally bacilliform 3−5.5 × 1.5−2 Marin-Felix et al. (2019)
A. siamensis glabrous, ovoid 70−90 × 68−85 3−6 × 4−5 hyaline, cylindrical, aseptate 3−4 × 2−3 Jayasiri et al. (2019)
A. thunbergiae subglobose to irregular, dark brown 39−200 × 48−230 4.5−7 × 4−5 oblong to cylindrical, incidentally slightly obovoid 3−5 × 1.5−2.5 this study
A. tropica subglobose 100−300 2−6 × 3−6 ellipsoidal 3−4 × 1−2 Boerema et al. (2004)
A. zantedeschiae subglobose or depressed 90−180 - oval or ellipsoidal 4−7 × 2.5−3.5 Boerema (1993)
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Supplementary Material

XML Treatment for Allophoma thunbergiae
BDJ.9.e63643-treatment1.xml (9.4KB, xml)
XML Treatment for Allophoma pterospermicola
BDJ.9.e63643-treatment2.xml (9.2KB, xml)

Acknowledgements

We would like to thank Dr. Danny Haelewaters and Ms. Subodini N. Wijesinghe for their meticulous reviews. This research is supported by the following funding sources: National Natural Science Foundation of China (nos. 31972222, 31660011), Program of Introducing Talents of Discipline to Universities of China (111 Program, D20023), Talent Project of Guizhou Science and Technology Cooperation Platform ([2017]5788-5, [2019]5641, [2019]13), Guizhou Science, Technology Department of International Cooperation Base Project ([2018]5806), the Project of Guizhou Provincial Education Department ([2020]001) and Guizhou Science and Technology Innovation Talent Team Project ([2020]5001). Nalin N. Wijayawardene acknowledges the National Natural Science Foundation of China (No: 31950410558) and Guizhou Medical University (grant number FAMP201906K).

References

  1. An Yuan Yan, Zeng Xiang Yu, Geng Kun, Hyde Kevin D, Wang Yong. One new species and one new record of Zasmidium in China. Biodiversity Data Journal. 2021;9 doi: 10.3897/BDJ.9.e59001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Aveskamp M M, De Gruyter J, Crous P W. Biology and recent developments in the systematics of Phoma, a complex genus of major quarantine significance. Fungal Diversity. 2008;31:1–18. [Google Scholar]
  3. Aveskamp M M, De Gruyter J, Woudenberg J H C, Verkley G J M, Crous Pedro W. Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera. Studies in Mycology. 2010;65 doi: 10.3114/sim.2010.65.01. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Babaahmadi Golnoosh, Mehrabi-Koushki Mehdi, Hayati Jamshid. Allophoma hayatii sp. nov., an undescribed pathogenic fungus causing dieback of Lantana camara in Iran. Mycological Progress. 2018;17(3) doi: 10.1007/s11557-017-1360-7. [DOI] [Google Scholar]
  5. Boerema G H. Contributions towards a monograph of Phoma (Coelomycetes)—II. Section peyronellaea. Persoonia-Molecular Phylogeny and Evolution of Fungi. 1993;15(2) [Google Scholar]
  6. Boerema G H, Gruyter J D, Noordeloos M E, Hamers M E C. Phoma identification manual. Differentiation of specific and infra-specific taxa in culture. CABI. 2004 doi: 10.1079/9780851997438.0000. [DOI]
  7. Cheek Martin, Nic Lughadha Eimear, Kirk Paul, Lindon Heather, Carretero Julia, Looney Brian, Douglas Brian, Haelewaters Danny, Gaya Ester, Llewellyn Theo, Ainsworth A. Martyn, Gafforov Yusufjon, Hyde Kevin D, Crous Pedro W, Hughes Mark, Forzza Rafaela Campostrini, Wong Khoon Meng, Walker Barnaby E, Niskanen Tuula. New scientific discoveries: Plants and fungi. Plants People Planet. 2020;2(5):371–388. doi: 10.1002/ppp3.10148. [DOI] [Google Scholar]
  8. Chen Q, Jiang J R, Zhang G Z, Cai L, Crous Pedro W. Resolving the Phoma enigma. Studies in Mycology. 2015;82 doi: 10.1016/j.simyco.2015.10.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chen Q, Hou L W, Duan W J, Crous P W, Cai L. Didymellaceae revisited. Studies in Mycology. 2017;87 doi: 10.1016/j.simyco.2017.06.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Crous Pedro W, Gams Walter, Stalpers Joost A, Robert Vincent, Stegehuis Gerrit. MycoBank: an online initiative to launch mycology into the 21st century. Studies in Mycology. 2004;50(1):19–22. [Google Scholar]
  11. Darriba Diego, Taboada Guillermo L, Doallo Ramón, Posada David. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods. 2012;9(8):772–772. doi: 10.1038/nmeth.2109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. De Gruyter J, Noordeloos M E. Contributions towards a monograph of Phoma (Coelomycetes)—I. 1. Section Phoma: Taxa with very small conidia in vitro. Persoonia-Molecular Phylogeny and Evolution of Fungi. 1992;15(1) [Google Scholar]
  13. De Gruyter Johannes, Aveskamp Maikel M, Woudenberg Joyce H C, Verkley Gerard JM, Groenewald Johannes Z, Crous Pedro W. Molecular phylogeny of Phoma and allied anamorph genera: towards a reclassification of the Phoma complex. Mycological Research. 2009;113(4):508–519. doi: 10.1016/j.mycres.2009.01.002. [DOI] [PubMed] [Google Scholar]
  14. De Gruyter J, Woudenberg J H C, Aveskamp M M, Verkley G J M, Groenewald J Z, Crous P W. Redisposition of Phoma-like anamorphs in Pleosporales. Studies in Mycology. 2012;75:1–36. doi: 10.3114/sim0004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. De Hoog G S, Van den Ended A H G G. Molecular diagnostics of clinical strains of filamentous Basidiomycetes. Mycoses. 1998;41 doi: 10.1111/j.1439-0507.1998.tb00321.x. [DOI] [PubMed] [Google Scholar]
  16. Garibaldi Angelo, Gilardi Giovanna, Ortu G, Gullino Maria Lodovica. First report of leaf spot of lettuce (Lactuca sativa L.) caused by Phoma tropica in Italy. Plant Disease. 2012;96(9) doi: 10.1094/PDIS-04-12-0394-PDN. [DOI] [PubMed] [Google Scholar]
  17. Hongsanan S, Hyde K D, Phookamsak R, Wanasinghe D N, McKenzie E H C, Sarma V V, Boonmee S, Lücking R, Bhat D J, Liu N G, Tennakoon D S, Pem D, Karunarathna A, Jiang S H, Jones E B G, Phillips A J L, Manawasinghe I S, Tibpromma S, Jayasiri S C, Sandamali D S, Jayawardena R S, Wijayawardene N N, Ekanayaka A H, Jeewon R, Lu Y Z, Dissanayake A J, Zeng X Y, Luo Z L, Tian Q, Phukhamsakda C, Thambugala K M, Dai D Q, Chethana K W T, Samarakoon M C, Ertz D, Bao D F, Doilom M, Liu J K, Pérez-Ortega S, Suija A, Senwanna C, Wijesinghe S N, Konta S, Niranjan M, Zhang S N, Ariyawansa H A, Jiang H B, Zhang J F, Norphanphoun C, de Silva N I, Thiyagaraja V, Zhang H, Bezerra J D P, Miranda-González R, Aptroot A, Kashiwadani H, Harishchandra D, Sérusiaux E, Aluthmuhandiram J V S, Abeywickrama P D, Devadatha B, Wu H X, Moon K H, Gueidan C, Schumm F, Bundhun D, Mapook Ausana, Monkai J, Chomnunti P, Suetrong S, Chaiwan N, Dayarathne M C, Yang J, Rathnayaka A R, Bhunjun C S, Xu J C, Zheng J S, Liu G, Feng Y, Xie N. Refined families of Dothideomycetes: Dothideomycetidae and Pleosporomycetidae. Mycosphere. 2020;11(1) doi: 10.5943/mycosphere/11/1/13. [DOI] [Google Scholar]
  18. Hopple John S. Phylogenetic investigations in the genus Coprinus based on morphological and molecular characters. Duke University; 1994. [Google Scholar]
  19. Hou Ling Wei, Hernández-Restrepo Margarita, Groenewald Johannes Zacharias, Cai Lei, Crous Pedro W. Citizen science project reveals high diversity in Didymellaceae (Pleosporales, Dothideomycetes) MycoKeys. 2020;65 doi: 10.3897/mycokeys.65.47704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hou L W, Groenewald J Z, Pfenning L H, Yarden O, Crous P W, Cai L. The phoma-like dilemma. Studies in Mycology. 2020;96:309–396. doi: 10.1016/j.simyco.2020.05.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hyde Kevin D, Jeewon Rajesh, Chen Yi Jyun, Bhunjun Chitrabhanu S, Calabon Mark S, Jiang Hong Bo, Lin Chuan Gen, Norphanphoun Chada, Sysouphanthong Phongeun, Pem Dhandevi, Tibpromma Saowaluck, Zhang Qian, Doilom Mingkwan, Jayawardena Ruvishika S, Liu Jian Kui, Maharachchikumbura Sajeewa S N, Phukhamsakda Chayanard, Phookamsak Rungtiwa, Al-Sadi Abdullah M, Thongklang Naritsada, Wang Yong, Gafforov Yusufjon, Jones E B G, Lumyong Saisamorn. The numbers of fungi: is the descriptive curve flattening? Fungal Diversity. 2020 doi: 10.1007/s13225-020-00458-2. [DOI]
  22. Jayasiri S C, Hyde K D, Jones E B G, McKenzie E H C, Jeewon R, Phillips A J L, Bhat D J, Wanasinghe D N, Liu J K, Lu Y Z, Kang J C, Xu J, Karunarathna S C. Diversity, morphology and molecular phylogeny of Dothideomycetes on decaying wild seed pods and fruits. Mycosphere. 2019;10(1) [Google Scholar]
  23. Jeewon R, Hyde K D. Establishing species boundaries and new taxa among fungi: recommendations to resolve taxonomic ambiguities. Mycosphere. 2016;7(11):1669–1677. doi: 10.5943/mycosphere/7/11/4. [DOI] [Google Scholar]
  24. Katoh Kazutaka, Standley Daron M. A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics. 2016;32(13):1933–1942. doi: 10.1093/bioinformatics/btw108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Liu Yajuan J, Whelen Sally, Hall Benjamin D. Phylogenetic relationships among Ascomycetes: evidence from an RNA polymerse II subunit. Molecular Biology and Evolution. 1999;16(12):1799–1808. doi: 10.1093/oxfordjournals.molbev.a026092. [DOI] [PubMed] [Google Scholar]
  26. Long Hui, Zhang Qian, Hao Yuan Yuan, Shao Xian Qiang, Wei Xiao Xing, Hyde Kevin D, Wang Yong, Zhao De Gang. Diaporthe species in south-western China. MycoKeys. 2019;57 doi: 10.3897/mycokeys.57.35448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Marin-Felix Y, Groenewald J Z, Cai L, Chen Q, Marincowitz S, Barnes I, Bensch K, Braun U, Camporesi E, Damm U, de Beer Z. W, Dissanayake A, Edwards J, Giraldo A, Hern andez-Restrepo M, Hyde K D, Jayawardena R S, Lombard L, Luangsa-ard J, McTaggart A R, Rossman A Y, Sandoval-Denis M, Shen M, Shivas R G, Tan Y P, van der Linde E J, Wingfield M. J., Wood A R, Zhang J Q, Zhang Y, Crous P W. Genera of phytopathogenic fungi: GOPHY 1. Studies in Mycology. 2017;86:99–216. doi: 10.1016/j.simyco.2017.04.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Marin-Felix Yasmina, Hernández-Restrepo Margarita, Iturrieta-González I, García D, Gené J, Groenewald J Z, Cai L, Chen Q, Quaedvlieg W, Schumacher R K. Genera of phytopathogenic fungi: GOPHY 3. Studies in Mycology. 2019;94 doi: 10.1016/j.simyco.2019.05.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Miller Mark A, Pfeiffer Wayne, Schwartz Terri. Creating the CIPRES Science Gateway for inference of large phylogenetic trees; Proceeding of the 2010 gateway computing environments workshop (GCE), New Orleans, Louisiana; 2010. 7. [DOI] [Google Scholar]
  30. Nagarjun N, Suryanarayana V. Documentation, characterization and management of leaf spot of Syzygium cumini (L.) Skeels. Journal of Farm Sciences. 2016;29(3) [Google Scholar]
  31. Nylander J A A. MrModeltest v2. Evolutionary Biology Centre, Uppsala University, Uppsala 2004
  32. O'Neill Tim, Mayne Sarah. An unusual Phoma stem rot of a tomato. AHDB Horticulture; 2016. [Google Scholar]
  33. Phukhamsakda Chayanard, McKenzie Eric H C, Phillips Alan J L, Gareth Jones E B, Jayarama Bhat D, Stadler Marc, Bhunjun Chitrabhanu S, Wanasinghe Dhanushka N, Thongbai Benjarong, Camporesi Erio, Ertz Damien, Jayawardena Ruvishika S, Perera Rekhani Hansika, Ekanayake Anusha H, Tibpromma Saowaluck, Doilom Mingkwan, Xu Jianchu, Hyde Kevin D. Microfungi associated with Clematis (Ranunculaceae) with an integrated approach to delimiting species boundaries. Fungal Diversity. 2020;102(1):1–203. doi: 10.1007/s13225-020-00448-4. [DOI] [Google Scholar]
  34. Rayner Ronald William. A mycological colour chart. CMI & British Mycological Society Kew Mycological Society, Kew; Surrey, UK: 1970. [Google Scholar]
  35. Ronquist Fredrik, Teslenko Maxim, Van Der Mark Paul, Ayres Daniel L, Darling Aaron, Höhna Sebastian, Larget Bret, Liu Liang, Suchard Marc A, Huelsenbeck John P. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology. 2012;61(3):539–542. doi: 10.1093/sysbio/sys029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Stamatakis Alexandros. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313. doi: 10.1093/bioinformatics/btu033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sung Gi Ho, Sung Jae Mo, Hywel-Jones Nigel L, Spatafora Joseph W. A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): Identification of localized incongruence using a combinational bootstrap approach. Molecular Phylogenetics and Evolution. 2007;44(3) doi: 10.1016/j.ympev.2007.03.011. [DOI] [PubMed] [Google Scholar]
  38. Swofford D L. PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4.0 b10. MA: Sinauer Associates, Sunderland, UK 2002
  39. Tamura Koichiro, Stecher Glen, Peterson Daniel, Filipski Alan, Kumar Sudhir. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution. 2013;30(12):2725–2729. doi: 10.1093/molbev/mst197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Valenzuela-Lopez N, Cano-Lira J F, Guarro J, Sutton Deanna A, Wiederhold Nathan, Crous P W, Stchigel A M. Coelomycetous Dothideomycetes with emphasis on the families Cucurbitariaceae and Didymellaceae. Studies in Mycology. 2018;90: 1-69 doi: 10.1016/j.simyco.2017.11.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Vilgalys Rytas, Hester Mark. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology. 1990;172(8):4238–4246. doi: 10.1128/JB.172.8.4238-4246.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. White Thomas J, Bruns Thomas, Lee S J W T, Taylor John. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Shinsky J, White T, editors. PCR protocols: a guide to methods and applications. Academic Press; NewYork: 1990. 315-322. [DOI] [Google Scholar]
  43. Wijayawardene Nalin N., Hyde Kevin D., Rajeshkumar Kunhiraman C., Hawksworth David L., Madrid Hugo, Kirk Paul M., Braun Uwe, Singh Rajshree V., Crous Pedro W., Kukwa Martin, Lücking Robert, Kurtzman Cletus P., Yurkov Andrey, Haelewaters Danny, Aptroot André, Lumbsch H. Thorsten, Timdal Einar, Ertz Damien, Etayo Javier, Phillips Alan J. L., Groenewald Johannes Z., Papizadeh Moslem, Selbmann Laura, Dayarathne Monika C., Weerakoon Gothamie, Jones E. B. Gareth, Suetrong Satinee, Tian Qing, Castañeda-Ruiz Rafael F., Bahkali Ali H., Pang Ka-Lai, Tanaka Kazuaki, Dai Dong Qin, Sakayaroj Jariya, Hujslová Martina, Lombard Lorenzo, Shenoy Belle D., Suija Ave, Maharachchikumbura Sajeewa S. N., Thambugala Kasun M., Wanasinghe Dhanushka N., Sharma Bharati O., Gaikwad Subhash, Pandit Gargee, Zucconi Laura, Onofri Silvano, Egidi Eleonora, Raja Huzefa A., Kodsueb Rampai, Cáceres Marcela E. S., Pérez-Ortega Sergio, Fiuza Patrícia O., Monteiro Josiane Santana, Vasilyeva Larissa N., Shivas Roger G., Prieto Maria, Wedin Mats, Olariaga Ibai, Lateef Adebola Azeez, Agrawal Yamini, Fazeli Seyed Abolhassan Shahzadeh, Amoozegar Mohammad Ali, Zhao Guo Zhu, Pfliegler Walter P., Sharma Gunjan, Oset Magdalena, Abdel-Wahab Mohamed A., Takamatsu Susumu, Bensch Konstanze, de Silva Nimali Indeewari, De Kesel André, Karunarathna Anuruddha, Boonmee Saranyaphat, Pfister Donald H., Lu Yong-Zhong, Luo Zong-Long, Boonyuen Nattawut, Daranagama Dinushani A., Senanayake Indunil C., Jayasiri Subashini C., Samarakoon Milan C., Zeng Xiang-Yu, Doilom Mingkwan, Quijada Luis, Rampadarath Sillma, Heredia Gabriela, Dissanayake Asha J., Jayawardana Ruvishika S., Perera Rekhani H., Tang Li Zhou, Phukhamsakda Chayanard, Hernández-Restrepo Margarita, Ma Xiaoya, Tibpromma Saowaluck, Gusmao Luis F. P., Weerahewa Darshani, Karunarathna Samantha C. Notes for genera: Ascomycota. Fungal Diversity. 2017;86(1):1–594. doi: 10.1007/s13225-017-0386-0. [DOI] [Google Scholar]
  44. Wijayawardene N N, Hyde K D, Al-Ani L K T, Tedersoo L, Haelewaters Danny, Rajeshkumar K C, Zhao R L, Aptroot A, Leontyev D, Saxena R K, Tokarev Y S, Dai D Q, Letcher P M, Stephenson S L, Ertz D, Lumbsch H T, Kukwa M, Issi I V, Madrid H, Phillips A J L, Selbmann L, Pfliegler W P, Horváth E, Bensch K, Kirk P M, Kolaříková K, Raja H A, Radek R, Papp V, Dima V, Ma J, Malosso E, Takamatsu S, Rambold G, Gannibal P B, Triebel D, Gautam A K, Avasthi S, Suetrong S, Timdal，E, Fryar S C, Delgado G, Réblová M, Doilom M, Dolatabadi S, Pawłowska J Z, Humber R A, Kodsueb R, Sánchez-Castro I, Goto B T, Silva D K A, de Souza F A, Oehl F, da Silva G A, Silva I R, Błaszkowski J, Jobim K, Maia L C, Barbosa F R, Fiuza P O, Divakar P K, Shenoy B D, Castañeda-Ruiz R F, Somrithipol S, Lateef A A, Karunarathna S C, Tibpromma S, Mortimer P E, Wanasinghe D N, Phookamsak R, Xu J, Wang Y, Tian F, Alvarado P, Li D W, Kušan I, Matočec N, Mešić A, Tkalčec Z, Maharachchikumbura S S N, Papizadeh M, Heredia G, Wartchow F, Bakhshi M, Boehm E, Youssef N, Hustad V P, Lawrey J D, Santiago A L C M A, Bezerra J D P, Souza-Motta C M, Firmino A L, Tian Q, Houbraken J, Hongsanan S, Tanaka K, Dissanayake A J, Monteiro J S, Grossart H P, Suija A, Weerakoon G, Etayo J, Tsurykau A, Vázquez V, Mungai P, Damm U, Li Q R, Zhang H, Boonmee S, Lu Y Z, Becerra A G, Kendrick B, Brearley F Q, Motiejūnaitė J, Sharma B, Khare R, Gaikwad S, Wijesundara D S A, Tang L Z, He M Q, Flakus A, Rodriguez-Flakus P, Zhurbenko M P, McKenzie E H C, Stadler M, Bhat D J, Liu J K, Raza M, Jeewon R, Nassonova E S, Prieto M, Jayalal R G U, Erdoğdu M, Yurkov A, Schnittler M, Shchepin O N, Novozhilov Y K, Silva-Filho A G S, Gentekaki E, Liu P, Cavender J C, Kang Y, Mohammad S, Zhang L F, Xu R F, Li Y M, Dayarathne M C, Ekanayaka A H, Wen T C, Deng C Y, Pereira O L, Navathe S, Hawksworth D L, Fan X L, Dissanayake L S, Kuhnert E, Grossart H P, Thines M. Outline of Fungi and fungus-like taxa. Mycosphere. 2020;11(1):1060–1456. doi: 10.5943/mycosphere/11/1/8. [DOI] [Google Scholar]
  45. Woudenberg J H C, Aveskamp M M, De Gruyter J, Spiers A G, Crous P W. Multiple Didymella teleomorphs are linked to the Phoma clematidina morphotype. Persoonia. 2009;22 doi: 10.3767/003158509X427808. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Zhang Qian, Wijayawardene Nalin N, Hyde Kevin D, Wang Yong, Pan Xue Jun. Xepicula yifeii sp. nov. caused a leaf blight of Lasia spinosa (Araceae) in South China karst. European Journal of Plant Pathology. 2020;158(1) doi: 10.1007/s10658-020-02060-3. [DOI] [Google Scholar]
  47. Zhang Qian, Yang Zai Fu, Cheng Wei, Wijayawardene Nalin N, Hyde Kevin D, Chen Zhuo, Wang Yong. Diseases of Cymbopogon citratus (Poaceae) in China: Curvularia nanningensis sp. nov. MycoKeys. 2020;63 doi: 10.3897/mycokeys.63.49264. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Zimowska Beata. Characteristics and occurrence of Phoma spp. on herbs from the family Lamiaceae. Acta Scientiarum Polonorum, Hortorum Cultus. 2011;10(2) [Google Scholar]

Associated Data

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Supplementary Materials

XML Treatment for Allophoma thunbergiae
BDJ.9.e63643-treatment1.xml (9.4KB, xml)
XML Treatment for Allophoma pterospermicola
BDJ.9.e63643-treatment2.xml (9.2KB, xml)

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