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19 May 2021

Multi-Gene Phylogeny and Morphology Reveal Haplohelminthosporium gen. nov. and Helminthosporiella gen. nov. Associated with Palms in Thailand and A Checklist for Helminthosporium Reported Worldwide

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1
CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
2
Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
3
School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
4
Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
This article belongs to the Special Issue Biodiversity and Ecology of Fungi in Terrestrial and Marine Ecosystems

Abstract

Palms (Arecaceae) are substrates for a highly diverse range of fungi. Many species are known as saprobes and many are important plant pathogens. Over the course of our studies of micro-fungi from palms in Thailand, two new taxa were discovered. Morphological characteristics and phylogenetic analyses of combined ITS, LSU, SSU, and tef1-α sequence data revealed their taxonomic positions within Massarinaceae. There are currently ten genera identified and accepted in Massarinaceae, with the addition of the two new genera of Haplohelminthosporium and Helminthosporiella, that are introduced in this paper. Each new genus is provided with a full description and notes, and each new taxon is provided with an illustration for the holotype. A list of identified and accepted species of Helminthosporium with morphology, host information, locality, sequence data, and related references of Helminthosporium reported worldwide is provided based on records in Species Fungorum 2021. This work provides a micro-fungi database of Haplohelminthosporium, Helminthosporiella, and Helminthosporium which can be modified and validated as new data come to light.

1. Introduction

In Thailand, a large number of novel fungi from a variety of hosts have been recently described, adding to the region’s highly known fungal diversity [,]. This diversity is supported by various factors, including host–plant species relationships, geography, seasons, air humidity, and temperature. Many interesting fungi from Thai monocotyledons such as bamboo (Poaceae) and Pandanaceae have been described in previous studies, and some new taxa and records of microfungi on palms have been published, especially from the southern region of Thailand [,,,,,,,,]. However, more research on fungal diversity on palms in Thailand is needed.
Pleosporales is the largest order in Dothideomycetes [] with 566 genera in 91 families accepted, while 48 genera have been placed in Pleosporales genera incertae sedis with an estimated stem age of 205 MYA [,]. Massarinaceae is a family within Pleosporales introduced by Munk [] to accommodate the genus Massarina, with M. eburnea being designated as the type species and described based on the sexual morph []. Hongsanan et al. [] and Wijayawardene et al. [] accepted nine genera in Massarinaceae (Byssothecium, Helminthosporiella, Helminthosporium, Massarina, Pseudodidymosphaeria, Pseudosplanchnonema, Semifissispora, Stagonospora, and Suttonomyces).
Helminthosporium has the asexual morph of H. velutinum as the type species. It is characterized by terminal and intercalary conidiogenous cells as well as solitary conidia with distosepta []. The members of this genus are commonly found as saprobes and endophytes, but they are often isolated from dead corticated twigs or wood, living leaves, and soils [,,,,,,]. Most Helminthosporium species have been described based on their asexual morph, and only a few species have been described based on both morphs viz., H. massarinum, H. microsorum, H. oligosporum, H. quercicola, H. quercinum, and H. tiliae [,,]. Several species in the Helminthosporium complex are polyphyletic and have been placed in other genera viz. Bipolaris, Curvularia, and Exserohilum within Pleosporales, other families viz. Corynesporaceae, Massarinaceae, and Mycosphaerellaceae within Dothideomycetes, or other unrelated Ascomycetes groups that were initially based on morphological characteristics and later on molecular data, although some species still remain unresolved [,,,,,,,,,,,,,]. Wijayawardene et al. [] approximated the number of taxa in Helminthosporium at 416 species. However, this genus was not updated with the DNA sequencesin the most recent monograph.
Few previous studies have investigated the Helminthosporium-like taxa from plants, particularly palms, in Thailand. In this study, we were able to isolate Helminthosporium-like taxa from palms collected in Thailand. Morphology and multi-gene phylogenetic analyses showed two Helminthosporium-like taxa are novel in Massarinaceae. In addition, we provide a checklist of Helminthosporium and the name for Helminthosporiella stilbacea is also validated.

2. Materials and Methods

2.1. Collection, Isolation, and Identification

The plant materials containing the fungal structures were collected from Krabi and Prachuap Khiri Khan Provinces, Thailand, from living and dead parts of palm trees (Calamus sp. and Cocos nucifera). Samples were taken to the laboratory for morphological study following the methods provided by Konta et al. []. Single spore isolates were obtained following the method of Senanayake et al. []. Measurements were taken using an Image Framework program. Illustrations were made in Adobe Photoshop CS6. Specimens and cultures were deposited in the herbarium of Mae Fah Luang University (MFLU) and Mae Fah Luang Culture Collection (MFLUCC). Faces of Fungi and Index Fungorum numbers were registered as outlined in Jayasiri et al. [] and Index Fungorum [], respectively.

2.2. DNA Extraction and Amplification (PCR)

DNA extraction was performed using the Biospin Fungus genomic DNA extraction kit-BSC14S1 (Bioflux, P.R. China) according to Dissanayake et al. []. Partial nucleotide genes were subjected to PCR amplification and sequencing of the large subunit (28S, LSU) [], the internal transcribed spacer (ITS) [], the small subunit (18S, SSU) [], and the translation elongation factor 1-alpha (tef1-α) was performed [,]. For primers and conditions, see Table 1. PCR amplification and sequencing were carried out following Konta et al. []. The resulting fragments were sequenced in both forward and reverse directions, the generated DNA sequences were analysed, and the consensus sequences were computed using SeqMan software. New sequences generated in this study were deposited in GenBank (Table 2).
Table 1. Details of genes/loci with PCR primers and PCR conditions.

2.3. Phylogenetic Analyses

The sequences generated in this study were subjected to a BLAST search in GenBank to identify closely related sequences. Sequence data retrieved from GenBank and recent publications were used as references []. Sequence data for the ITS, LSU, SSU, and tef1-α regions were analysed both individually and in combination. A total of 93 taxa were used for the combined phylogenetic analyses (ITS, LSU, SSU, and tef1-α) in order to find a natural classification placement. In addition, 103 taxa of ITS and 113 taxa of LSU were used for phylogenetic analyses. For both the individual and combined phylogenetic analyses, Cyclothyriella rubronotata (Cyclothyriellaceae) was selected as the outgroup taxon. Absent sequence data (i.e., ITS, LSU, SSU, tef1-α sequence data) in the alignments were treated with gaps as missing data. Sequence alignments were carried out with MAFFT v.6.864b [] and were manually improved where necessary. The single gene datasets were combined using Mega7 []. Data were converted from fasta to nexus and PHYLIP format with Alignment Transformation Environment online, https://sing.ei.uvigo.es/ALTER/ (accessed on 15 July 2020) []. The tree topologies obtained from single gene sequence data were compared prior to the combined gene analysis in order to check for incongruence in the overall topology of the phylogenetic tree. Maximum likelihood (ML) analysis was accomplished using RAxML-HPC2 (v.8.2.12) on XSEDE in the CIPRES Science Gateway platform (http://www.phylo.org) (accessed on 12 May 2020) [] with GTRGAMMA model and set as 1000 bootstrap replicates. Bayesian analysis was performed at CIPRES using Bayesian analysis on XSEDE (v.3.2.7) as part of the “MrBayes on XSEDE” tool [,,]. GTR+I+G model was selected by using MrModelTest 2.2 [] under the Akaike information criterion (AIC) as the best-fit models of the combined dataset for maximum likelihood and Bayesian analysis []. Bayesian posterior probabilities (BYPP) were determined by Markov Chain Monte Carlo sampling (MCMC) in MrBayes on XSEDE v.3.2.7. Six simultaneous Markov chains were run for 5,000,000 generations and trees were sampled every 1000th generation. An MCMC heated chain was set with a “temperature” value of 0.20. All sampled topologies beneath the asymptote (25%) were discarded as part of a burn-in procedure; the remaining trees (7502) were used for calculating posterior probabilities in the majority rule consensus tree. Bootstrap support values for ML and BYPP are given near to each node (Figure 1 and Figure 2). The phylogenetic trees were configured in FigTree v1.4.0 [] and edited using Microsoft Office PowerPoint 2016 and Adobe Photoshop CS6 (Adobe Systems, San Jose, CA, USA).
Figure 1. Comparison of the topology of Maximum likelihood majority rule consensus tree for the analyses of some selected Corynesporaceae, Massarinaceae, and Perioconiaceae isolates. (A) Phylogenetic tree of the dataset for ITS sequence data. (B) Phylogenetic tree of the dataset for LSU sequence data. Bootstrap support values for maximum likelihood (ML) equal to or higher than 50%, and Bayesian Posterior Probabilities (BYPP) equal to or greater than 0.90 are given above each branch. Novel taxa are in blue. Ex-type strains are in bold. The tree is rooted to Cyclothyriella rubronotata strains TR, TR9 (Cyclothyriellaceae).
Figure 2. Maximum likelihood majority rule consensus tree for the analyses of Massarinaceae and sister family Perioconiaceae isolates based on a dataset of combined ITS, LSU, SSU, and tef1-α sequence data. Bootstrap support values for maximum likelihood (ML) equal to or higher than 50%, and Bayesian posterior probabilities (BYPP) equal to or greater than 0.90 are given above each branch. Novel taxa are in blue. Ex-type strains are in bold. The tree is rooted to Cyclothyriella rubronotata strains TR, TR9 (Cyclothyriellaceae).
Table 2. Taxa names, strain numbers and GenBank accession numbers of the sequences used in phylogenetic analyses.
Table 2. Taxa names, strain numbers and GenBank accession numbers of the sequences used in phylogenetic analyses.
FamilySpeciesStrain No.GenBank Accession No.References
ITSLSUSSUtef1-α
CorynesporaceaeCorynespora cassiicolaCBS 100,822 -GU301808GU296144GU349052[]
CorynesporaceaeCorynespora cassiicolaCCPKF810854-GU296145-[,]
CorynesporaceaeCorynespora smithiiCBS 139,925 KY984299KY984299--[]
CorynesporaceaeCorynespora smithiiL120 KY984297KY984297-KY984435[]
CorynesporaceaeCorynespora smithiiL130 KY984298KY984298KY984419KY984436[]
CorynesporaceaeCorynespora smithiiL139KY984300KY984300--[]
CyclothyriellaceaeCyclothyriella rubronotataTR KX650541KX650541-KX650516[]
CyclothyriellaceaeCyclothyriella rubronotataTR9 * KX650544KX650544KX650507KX650519[]
MassariaceaeByssothecium circinansCBS 675.92-GU205217GU205235GU349061[]
MassarinaceaeByssothecium circinansCBS 675.92-AY016357AY016339-[,]
MassarinaceaeHaplohelminthosporium calamiMFLUCC 18-0074 *MT928158MT928156MT928160-This study
MassarinaceaeHelminthosporium aquaticumMFLUCC 15-0357KU697302KU697306KU697310-[]
MassarinaceaeHelminthosporium aquaticumDLUCC 0758 MG098779MG098786MG098795MG98585[]
MassarinaceaeHelminthosporium austriacumL132 * KY984301KY984301KY984420KY984437[]
MassarinaceaeHelminthosporium austriacumL169KY984303KY984303-KY984439[]
MassarinaceaeHelminthosporium austriacumL137 KY984302KY984302-KY984438[]
MassarinaceaeHelminthosporium caespitosumL99 * JQ044429JQ044448KY984421KY984440[]
MassarinaceaeHelminthosporium caespitosumL141 KY984305KY984305--[]
MassarinaceaeHelminthosporium caespitosumL151 KY984306KY984306--[]
MassarinaceaeHelminthosporium dalbergiaeH 4628 LC014555AB807521AB797231AB808497[]
MassarinaceaeHelminthosporium endiandraeCBS 138902 * KP004450KP004478--[]
MassarinaceaeHelminthosporium endiandraeCBS 138,902 -MH878637--[]
MassarinaceaeHelminthosporium endiandraeSM64 MT279335---Unpublished
MassarinaceaeHelminthosporium endiandraeSM61MT279339---Unpublished
MassarinaceaeHelminthosporium endiandraeSM64 MT279340---Unpublished
MassarinaceaeHelminthosporium endiandraeSM61MT279336---Unpublished
MassarinaceaeHelminthosporium endiandraeAKRM1MN880136---Unpublished
MassarinaceaeHelminthosporium erythrinicolaCBS 145,569 MK876391MK876432--[]
MassarinaceaeHelminthosporium genistaeL128 KY984308KY984308KY984422-[]
MassarinaceaeHelminthosporium genistaeL129 KY984309KY984309KY984423-[]
MassarinaceaeHelminthosporium genistaeL142 * KY984310KY984310--[]
MassarinaceaeHelminthosporium hispanicumL109 * KY984318KY984318KY984424KY984441[]
MassarinaceaeHelminthosporium italicumMFLUCC 17-0241KY797638KY815015-KY815021[]
MassarinaceaeHelminthosporium juglandinumL97 KY984322KY984322KY984425KY984445[]
MassarinaceaeHelminthosporium juglandinumL118 * KY984321KY984321-KY984444[]
MassarinaceaeHelminthosporium leucadendriCBS 135133 * KF251150KF251654-KF253110[]
MassarinaceaeHelminthosporium magnisporumH 4627 * AB811452AB807522AB797232AB808498[]
MassarinaceaeHelminthosporium massarinumKT 1564 * AB809629AB807524AB797234AB808500[]
MassarinaceaeHelminthosporium massarinumKT 838 AB809628AB807523AB797233AB808499[]
MassarinaceaeHelminthosporium microsorumL94 KY984327KY984327KY984426KY984446[]
MassarinaceaeHelminthosporium microsorumL95 KY984328KY984328-KY984447[]
MassarinaceaeHelminthosporium microsorumL96 * KY984329KY984329KY984427KY984448[]
MassarinaceaeHelminthosporium oligosporumL92 KY984332KY984332KY984428KY984450[]
MassarinaceaeHelminthosporium oligosporumL93 * KY984333KY984333-KY984451[]
MassarinaceaeHelminthosporium oligosporumL106 KY984330KY984330-KY984449[]
MassarinaceaeHelminthosporium quercinumL90 * KY984339KY984339KY984429KY984453[]
MassarinaceaeHelminthosporium quercinumL91 KY984340KY984340-KY984454[]
MassarinaceaeHelminthosporium solaniCBS 365.75 KY984341KY984341KY984430KY984455[]
MassarinaceaeHelminthosporium solaniCBS 640.85 KY984342KY984342--[]
MassarinaceaeHelminthosporiella stilbaceaCPHmZC-01KX228298KX228355--[]
MassarinaceaeHelminthosporiella stilbaceaCOAD 2126MG668862---[]
MassarinaceaeHelminthosporiella stilbaceaMFLUCC 15-0813 *MT928159MT928157MT928161MT928151This study
MassarinaceaeHelminthosporium submersumMFLUCC 16-1360 *-MG098787MG098796MG098586[]
MassarinaceaeHelminthosporium submersumMFLUCC 16-1290MG098780MG098788MG098797MG098587[]
MassarinaceaeHelminthosporium submersumDLUCC 0805 MG098781MG098789MG098798-[]
MassarinaceaeHelminthosporium syzygiiCBS 145,570 *MK876392MK876433--[]
MassarinaceaeHelminthosporium tiliaeL88 * KY984345KY984345KY984431KY984457[]
MassarinaceaeHelminthosporium tiliaeL89 KY984346KY984346--[]
MassarinaceaeHelminthosporium tiliaeL171KY984343KY984343-KY984456[]
MassarinaceaeHelminthosporium velutinumyone 38 -AB807527AB797237AB808502[]
MassarinaceaeHelminthosporium velutinumyone 63 -AB807528AB797238AB808503[]
MassarinaceaeHelminthosporium velutinumMFLUCC 15-0423KU697300KU697304KU697308-[]
MassarinaceaeHelminthosporium velutinumMFLUCC 15-0428KU697299KU697303KU697307-[]
MassarinaceaeHelminthosporium velutinumH 4626 LC014556AB807530AB797240AB808505[]
MassarinaceaeHelminthosporium velutinumL117 KY984349KY984349-KY984460[]
MassarinaceaeHelminthosporium velutinumL126 KY984350KY984350-KY984461[]
MassarinaceaeHelminthosporium velutinumL131 * KY984352KY984352KY984432KY984463[]
MassarinaceaeHelminthosporium velutinumCPC 26297= CBS 141,504 KX306757KX306785--[]
MassarinaceaeHelminthosporium velutinumyone 96 LC014558AB807529AB797239AB808504[]
MassarinaceaeHelminthosporium velutinumH 4739 LC014557AB807525AB797235AB808501[]
MassarinaceaeHelminthosporium velutinumL115 KY984347KY984347-KY984458[]
MassarinaceaeHelminthosporium velutinumL116 KY984348KY984348-KY984459[]
MassarinaceaeHelminthosporium velutinumL127KY984351KY984351-KY984462[]
MassarinaceaeHelminthosporium velutinumL98 KY984359KY984359KY984433KY984466[]
MassarinaceaeHelminthosporium velutinumH 4743 -AB807526AB797236-[]
MassarinaceaeHelminthosporium velutinumMFLUCC 16-1096MG098783MG098791MG098799MG098588[]
MassarinaceaeHelminthosporium velutinumMFLUCC 16-1282MG098784MG098792MG098800MG098589[]
MassarinaceaeHelminthosporium velutinumMFLUCC 17-1707MG098785MG098793MG098801MG098590[]
MassarinaceaeHelminthosporium velutinumMFLUCC 17-1321-MG098794MG098802MG098591[]
MassarinaceaeHelminthosporium velutinumS-076KU697301KU697305KU697309-[]
MassarinaceaeHelminthosporium velutinumMFLUCC 15-0243KU697301KU697305KU697309-[]
MassarinaceaeHelminthosporium velutinumMFLUCC 16-1300MG098782MG098790--[]
MassarinaceaeMassarina albocarnisCBS119345LC194503LC194379LC194337LC194416[]
MassarinaceaeMassarina cistiCBS 266.62 * LC014568AB807539AB797249AB808514[]
MassarinaceaeMassarina cistiCBS 266.62-FJ795447FJ795490-[]
MassarinaceaeMassarina eburneaCBS 473.64 AF383959GU301840AF164367-[,]
MassarinaceaeMassarina eburneaJCM 14422LC014569AB521735AB521718AB808517[]
MassarinaceaeMassarina igniariaCBS 845.96-FJ795452FJ795494-[]
MassarinaceaeMassarina pandanicolaMFLUCC 17-0596 MG646958MG646947MG646979MG646986[]
MassarinaceaeMassarina phragmiticolaCBS 110,446 -DQ813510DQ813512-[]
MassarinaceaeNeottiosporina paspaliCBS 331.37 -EU754172EU754073-[]
MassarinaceaePseudodidymosphaeria spartiiCBS 183.58 -GU205225GU205250-[]
MassarinaceaePseudodidymosphaeria spartiiMFLUCC 13-0273 KP325434KP325436KP325438-[]
MassarinaceaePseudodidymosphaeria spartiiMFLUCC 14-1212 KP325435KP325437KP325439-[]
MassarinaceaePseudosplanchnonema phorcioidesMFLUCC 14-0618KP683372KP683373KP683374-[]
MassarinaceaePseudosplanchnonema phorcioidesMFLUCC 13-0533-KM875454KM875455-[]
MassarinaceaePseudosplanchnonema phorcioidesL16KY984360-KY984434KY984467[]
MassarinaceaePseudosplanchnonema phorcioidesMFLUCC 13-0611KP683375KP683376KP683377-[]
MassarinaceaeSemifissispora natalisCPC 25383KT950846KT950858-KT950878[]
MassarinaceaeSemifissispora natalisCBS 140659-MH878157--[]
MassarinaceaeSemifissispora rotundataCPC 549 KT950847KT950859--[]
MassarinaceaeSemifissispora tooloomensisCBS143431MG38607MG386124--[]
MassarinaceaeStagonospora perfectaKT 1726A AB809642AB807579AB797289AB808555[]
MassarinaceaeStagonospora cf. paludosaCBS 130,005 KF251254KF251757--[]
MassarinaceaeStagonospora duoseptataCBS 135,093 KF251255KF251758--[]
MassarinaceaeStagonospora imperaticolaMFLUCC 15-0026KY706143KY706133KY706138KY706146[]
MassarinaceaeStagonospora multiseptataMFLUCC 15-0449KX965735KX954404--[]
MassarinaceaeStagonospora paludosaCBS 135088 * KF251257KF251760-KF253207[]
MassarinaceaeStagonospora perfectaCBS 135,099 KF251258KF251761--[]
MassarinaceaeStagonospora perfectaKT 1726A AB809642AB807579AB797289AB808555[]
MassarinaceaeStagonospora pseudocaricisCBS 135,132 KF251259KF251763--[]
MassarinaceaeStagonospora pseudopaludosaCPC 22,654 KF777188KF777239--[]
MassarinaceaeStagonospora pseudoperfectaKT 889 * AB809641AB807577AB797287AB808553[]
MassarinaceaeStagonospora sp.CBS 135,096 KF251263KF251766--[]
MassarinaceaeStagonospora tainanensisKT 1866AB809643AB807580AB797290AB808556[]
MassarinaceaeStagonospora trichophoricolaCBS 136,764 KJ869110KJ869168--[]
MassarinaceaeStagonospora uniseptataCPC 22,150 KF251266KF251769--[]
MassarinaceaeStagonospora uniseptataCBS 135,090 KF251264KF251767--[]
MassarinaceaeSuttonomyces clematidisMFLUCC 14-0240 -KP842917KP842920-[]
MassarinaceaeSuttonomyces rosaeMFLUCC 15-0051 MG828973MG829085MG829185-[]
PericoniaceaePericonia byssoidesH 4600 LC014581AB807570AB797280AB808546[]
PericoniaceaePericonia digitataCBS 510.77LC014584AB807561AB797271AB808537[]
PericoniaceaePericonia macrospinosaCBS 135,663 KP183999KP184038KP184080-[]
PericoniaceaePericonia pseudodigitataKT 1395 * LC014591AB807564AB797274AB808540[]
* = The asterisks after the strain number represent the ex-type strains from the holotype specimens.

3. Results and Discussion

3.1. Phylogenetic Analyses

The individual datasets for ITS and LSU regions comprised selected isolates from closely related families (Figure 1). The RAxML analyses of the ITS dataset yielded the best-scoring trees with a final ML optimization likelihood value of -9830.778478 (Figure 1A). The matrix had 531 distinct alignment patterns with 51.80% undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.227770, C = 0.273565, G = 0.243931, T = 0.254733; substitution rates AC = 2.172295, AG = 3.427213, AT = 2.029849, CG = 0.957843, CT = 5.859679, GT = 1.000000; and gamma distribution shape parameter α = 0.350193. In Figure 1A, the novel taxon Haplohelminthosporium calami grouped within Massarinaceae and was well separated from other genera but without good bootstrap support. Helminthosporiella stilbacea (MFLUCC 15-0813) is closely related to Hel.stilbacea (strains CPHmZC-01 and COAD 2126) with 100% ML/1.00 BYPP.
The RAxML analyses of the LSU dataset yielded the best-scoring trees with a final ML optimization likelihood value of −4283.882978 (Figure 1B). The matrix had 307 distinct alignment patterns with 12.16% undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.246483, C = 0.214075, G = 0.309890, T = 0.229553; substitution rates AC = 1.828869, AG = 4.019496, AT = 3.119987, CG = 0.662100, CT = 12.098644, GT = 1.000000; and gamma distribution shape parameter α = 0.159335. In Figure 1B, the novel taxon Haplohelminthosporium calami was also well separated within Massarinaceae and clustered with Helminthosporium and Helminthosporiella. Helminthosporiella stilbacea (MFLUCC 15-0813) is closely related to Hel. stilbacea (strain CPHmZC-01) with 100% ML/1.00 BYPP.
The RAxML analysis of the combined (ITS, LSU, SSU, and tef1-α) dataset yielded a best scoring tree with a final ML optimization likelihood value of -22122.846454 (Figure 2). The matrix had 1363 distinct alignment patterns, with 41.38% undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.241467, C = 0.241603, G = 0.271551, T = 0.245380; substitution rates AC = 1.860804, AG = 3.064520, AT = 1.916442, CG = 1.009390, CT = 7.530432, GT = 1.000000; and gamma distribution shape parameter α = 0.183588. In the phylogenetic analyses (Figure 2), twelve genera are included in the tree. The novel taxon of Haplohelminthosporium calami grouped within Massarinaceae without strong bootstrap support. Haplohelminthosporium calami is closely related to H. endiandrae (CBS 138902, MH878637), but this is statistically unsupported. Helminthosporiella stilbacea (MFLUCC 15-0813) constitutes a sister phylogenetic affiliation to Hel. stilbacea (strains CPHmZC-01 and COAD 2126) with 100% ML/1.00 BYPP statistical support.
The phylogenetic analyses (Figure 1 and Figure 2) showed several topologies of the tree had generally rather low support (ML ≤50% and BYPP ≤0.90). This reflects the relatively high amount of homoplasy in the data. Most Helminthosporium-like taxa did not have SSU and tef1-α sequence data for the phylogenetic analyses. In the future, divergent time estimations will be needed for Helminthosporium-like taxa to resolve taxonomic confusion and placement.

3.2. Taxonomy

3.2.1. Haplohelminthosporium Konta & K.D. Hyde, gen. nov

Index Fungorum number: IF557873; Facesoffungi number: FoF09169
Etymology—Haplo in Greek means single, which refers to the single conidium in each conidiophore. It is a close relative of Helminthosporium.
Saprobic on living leaves and petioles of Calamus sp. On living leaves, small spots, circular to irregular, yellow in the beginning, later becoming red brown surrounded by yellow. Colonies on natural substrate forming black patches on the upper leaf, petiole surfaces. Sexual morph: Undetermined. Asexual morph: Hyphomycetous. Colonies on natural substrate forming black patches on the upper leaf, petiole surfaces. Mycelium mostly immersed, partly on the surface forming small stroma-like aggregations of red brown pseudoparenchymatous cells. Conidiophores arising singly or fasciculate from stroma cells, erect, simple, unbranched, straight, curved and swollen at apex, septate, thick-walled, cylindrical, smooth, bulbous at base, hyaline in the middle, brown to yellow-brown at 1–2-cells above the base, pale brown to yellow-brown at apical cell. Conidiogenous cells monotretic, terminal, determinate, cylindrical, wide and yellow-brown with a well-defined, small, noncicatrized pore at the apex. Conidia one for each conidiophore, obpyriform to lageniform, straight or curved, smooth, olive-brown, distoseptate, with a dark scar at the base.
Type species—Haplohelminthosporium calami Konta & K.D. Hyde
Notes: Haplohelminthosporium is established as a monotypic genus with Hap. calami as the type species. ITS phylogenetic analyses separated this genus from other genera, while in the LSU and multigene analyses it clustered with Helminthosporium and Helminthosporiella, but both without good statistical support (Figure 1 and Figure 2). Haplohelminthosporium is presented herein as an asexual morph (hyphomycete) similar to Helminthosporium and Helminthosporiella in that it is hyphomycete with an erect conidiophore, monotretic conidiogenous cell and distoseptate conidia [,,]. The type species of Helminthosporium has pale to dark brown, septate conidiophores, with terminal and intercalary polytretic conidiogenous cells, noncicatrized pores at the apex and upper 3–4 cells, solitary or short catenate conidia that are subhyaline to brown, distoseptate, and is dark brown to black scar at the base []. Helminthosporiella has brown to red-brown conidiophores with terminal, polytretic conidiogenous cells, with catenate and easily disarticulating chains of conidia that are medium brown, striated at surface and distoseptate []. However, Haplohelminthosporium is distinguished by its unbranched conidiophores arising solitarily or fasciculate from the stroma-like bulbous basal cells that are hyaline in the middle, brown to red-brown at 1–2-cells above the base, pale brown to red-brown and curved at the apical cell with well-defined non-cicatrized small pores and with a single olive-brown conidium arising from each conidiophore (Figure 3). In the BLAST search of GenBank, the closest match of the LSU, ITS, and SSU sequence data were identical to Helminthosporium spp. Based on distinguishing morphological characteristics together with single/multigene phylogenetic analyses we introduce the newly described strain as a new genus Haplohelminthosporium in Massarinaceae.
Figure 3. Haplohelminthosporium calami (MFLU 20-0520, holotype) (A) The forest in Krabi Province. (BE) Fresh and herbarium palm samples. (F,G) Colonies on living leaf. (HL) Conidiophores. (MU) Conidia. (V,W) Germinated conidia. (X) Culture on PDA. (Y) Conidiophore and conidia on culture. (Z) Conidiogenesis. (AA) Conidiophores. (AB,AC) Conidia. Scale bars: C, E =2 cm, H–W, Y–AC = 50 μm.
Haplohelminthosporium calami Konta & K.D. Hyde, sp. nov.
Index Fungorum number: IF557874, Facesoffungi number: FoF09170, Figure 3
Etymology: Referring to the genus of palm trees Calamus L.
Holotype: MFLU 20-0520.
Saprobic on living leaves and petioles of Calamus sp. On living leaves, small spots, circular to irregular, yellow in the beginning, later becoming red-brown surrounded by yellow. Colonies on natural substrate forming black patches on the upper leaf, petiole surfaces. Sexual morph: Undetermined. Asexual morph: Mycelium mostly immersed, on the surface forming small stroma-like aggregations of red brown pseudoparenchymatous stromal cells (7–)10–14(–20) μm ( x ¯ = 12 μm). Conidiophores (110–)140–175(–215) × (4–)5–7(–8) μm ( x ¯ = 160 × 6 μm, n = 50), wide at the base and apex, macronematous, mononematous, arising singly or fasciculate from the stroma cells, erect, simple, unbranched, straight, curved and swollen at the apex, thick-walled, cylindrical, smooth, bulbous at base, hyaline in the middle, brown to red-brown at 1–2-cells above the base, pale brown to red brown at the last cell of the apex, (3–)4–5(–6) septa. Conidiogenous cells monotretic, terminal, determinate, cylindrical, with well-defined small noncicatrized pores at the apex, wide and yellow-brown at the apex. Conidia (55–)70–100(–120) × (13–)17–20(–23) μm ( x ¯ = 80 × 20 μm, n = 60), one on each conidiophore, obpyriform to lageniform, straight or curved, smooth, olive-brown, (3–)4–6(–7)-distoseptate, with a dark scar at the base.
Culture characteristics: Culture on PDA, colony yellow-gray-brown at the center, turning dull creamy white toward to margin, smooth, dense, zonate at the margin (Figure 3X).
Material examined: THAILAND, Krabi Province, on living leaves and petioles of Calamus sp. (Arecaceae), 14 December 2015, Sirinapa Konta, KHNPR-2 (MFLU 20-0520, holotype); ex-type living culture, MFLUCC 18-0074.
Notes: BLAST search of the ITS sequence of the newly described strain (Haplohelminthosporium calami) shows 88.89% similarity with Helminthosporium juglandinum (L118), the LSU sequence shows 98.75% similarity with H. aquaticum (MFLUCC 15-0357), and the SSU sequence shows 99.52% similarity with H. quercinum (L90). Based on ITS phylogenetic analysis, Haplohelminthosporium calami formed a single branch at the basal clades of Helminthosporiella and Helminthosporium (Figure 1A), while based on LSU analysis, Hap. calami clustered together with H. juglandinum (L97), H. endiandrae (CBS 138902, MH878637), and Hel. stilbacea with no strong statistical support for both analyses. The phylogenetic results of the combined dataset indicated that Hap. calami clustered with H. endiandrae (CBS 138902, MH878637) without strong bootstrap support (Figure 2). Comparison of base pair differences between LSU loci for isolates of Hap. calami strains MFLUCC 18-0074 and H. endiandrae strains CBS 138,902 (KP004478; Ex-type from the holotype, and MH878637; sister strain) including gaps showed 1.74% (15/861 bp) differences, and the position of each base pair difference is shown in Table 3. Other H. endiandrae strains (AKMR1, CBS 138902; ex-type from the holotype, and SM61) grouped together in Helminthosporium, as the other strains have an ITS region, but the H. endiandrae (CBS 138902, MH878637) strain that grouped with our new collection lacks the ITS region. Therefore, we compared the morphology of these two species and found that Hap. calami differs from H. endiandrae with respect to its smaller conidiophores ((110–)140–175(–215) × (4–)5–7(–8) vs. 200–300 × 5–7 μm), number of conidiophore septa ((3–)4–5(–6) vs. 8–16 septa), larger conidia ((55–)70–100(–120) × (13–)17–20(–23) vs. (35–)37–45(–57) × (7–)8(–9) μm), solitary conidium per conidiophore, and higher number of distoseptate ((3–)4–6(–7)-distoseptate vs. 3(–4)-distoseptate). The results show the placement of Haplohelminthosporium calami within Massarinaceae, and that this species is distinct from other known species. Therefore, we introduce Hap. Calami as a new species based on both morphological and phylogenetic data.
Table 3. Polymorphic nucleotides from sequence data of the LSU loci for isolates of Haplohelminthosporium calami MFLUCC 18-0074 and Helminthosporium endiandrae CBS 138,902 (KP004478, MH878637).

3.2.2. Helminthosporiella Konta & K.D. Hyde, gen. nov.

Index Fungorum number: IF558311, Facesoffungi number: FoF09171
Helminthosporiella Hern.-Restr., Sarria & Crous, in Crous et al., Persoonia 36: 437 (2016), MycoBank MB816988, Nom. inval., Art. 40.3 (Shenzhen)
Saprobic on dead petiole of Cocos nucifera.Sexual morph: Undetermined. Asexualmorph:Colony on natural substrate black, hairy. Mycelium mostly immersed, at the surface forming small stroma-like aggregations of dark brown pseudoparenchymatous cells. Conidiophores macronematous, wide at the apex and base, arising singly from the stroma cells, erect, simple, unbranched, straight or flexuous, thick-walled, cylindrical, smooth-walled, dark brown, becoming pale brown at the apex, septate. Conidiogenous cells terminal and intercalary, polytretic, with well-defined thick, pale brown pores. Conidia obpyriform to lageniform, straight or curved, smooth-walled, subhyaline to light brown, distoseptate, with a thick scar at the base.
Type species—Helminthosporiella stilbacea Konta & K.D. Hyde
Notes: Helminthosporiella was introduced by Crous et al. [] to accommodate a new combination of Hel. stilbacea Hern.-Restr., Sarria & Crous, in Massarinaceae, the basionym of the type species was not provided a Latin diagnosis []. In this paper we accept Helminthosporiella as a distinct genus, presently with a single species Helminthosporiella stilbacea. Since a Latin diagnosis is no longer required, we provide an English diagnosis and priority was given to the previous genus and species names. Furthermore, this study provides the holotype to validate the genus and species, and reports the first host record of Hel. stilbacea associated with coconut tree (Arecaceae) in Thailand. In particular, based on the present morphology and DNA sequence data, Helminthosporiella is identified as a monotypic genus, with Hel. stilbacea as the type species. The members of Helminthosporiella were found associated with leaf spots on oil palm (Arecaceae) [].
Helminthosporiella stilbacea Konta & K.D. Hyde, sp. nov.
Index Fungorum number: IF558312, Facesoffungi number: FoF09172, Figure 4.
Figure 4. Helminthosporiella stilbacea (MFLU 20-0521, holotype) (A) A coconut plantation in Prachuap Khiri Khan Province. (B) Palm samples. (CE) Conidiogenesis. (FH) Conidiophores (at red arrow are pores). (IM) Conidia. (N,O) Germinated conidia. (P) Culture on MEA. Scale bars: B = 2 cm, C, I–O = 20 μm, D–H = 50 μm.
=Cercospora palmicola f. stilbacea Moreau, Rev. Mycol. 12: 38. 1947 Nom. inval., Art. 39.1 (Shenzhen)
Helminthosporiella stilbacea Hern.-Restr., Sarria & Crous, in Crous et al., Persoonia 36: 437. 2016; Nom. inval., Art. 39.1 (Shenzhen)
Helminthosporium stilbaceum Moreau ex S. Hughes, Mycol. Pap.48: 38. 1952; Nom. inval., Art. 39.1 (Shenzhen).
Exosporium stilbaceum Moreau ex M.B. Ellis, Mycol. Pap.82: 38. 1961; Nom. inval., Art. 39.1 (Shenzhen).
=Exosporium stilbaceum var. macrosporum Subramon. & V.G. Rao, Journal of the Annamalai University, part B, Sciences 29: 404. 1971; Nom. inval., Art. 35.1 (Shenzhen).
Saprobic on dead petiole of Cocos nucifera.Sexual morph: Undetermined. Asexualmorph: Colony on natural substrate black, hairy. Mycelium mostly immersed, at the surface forming small stroma-like aggregations of dark brown pseudoparenchymatous cells (6–)11–15(–25) μm diam ( x ¯ = 14 μm). Conidiophores (60–)165–270(–310) × (5–)7–9(–12) μm ( x ¯ = 200 × 8 μm, n = 30), macronematous, wide at the apex and base, arising singly from the stroma cells, erect, simple, unbranched, straight or flexuous, thick-walled, cylindrical, smooth-walled, dark brown, becoming pale brown at the apex, (4–)12–15-septate. Conidiogenous cells terminal and intercalary, polytretic, with well-defined thick, pale brown pores. Conidia (30–)45–60(–70) × 6–9 μm ( x ¯ = 50 × 7 μm, n = 30), obpyriform to lageniform, straight or curved, smooth-walled, subhyaline to light brown, 5–8-distoseptate, with a thick scar at the base.
Culture characteristics: Culture on MEA, colony yellow-green at the center, turning dull green, pale yellow next, becoming dull green again, pale yellow, and white toward the margin. Colony smooth, dense at the middle, zonate, fluffy at the margin (Figure 4P).
Material examined: THAILAND, Prachuap Khiri Khan Province, on dead petiole of Cocos nucifera L. (Arecaceae), 30 July 2015, Sirinapa Konta PJK04gHB (MFLU 20-0521, holotype); ex-type living culture, MFLUCC 15-0813.
Notes: Crous et al. [] introduced a new genus Helminthosporiella with a new combination of Hel. stilbacea based on fresh collections from oil palm (Elaeis oleifera) in Colombia and the second collection of Hel. stilbacea was also collected from oil palm (Elaeis guineensis) in Brazil by Rosado et al. []. The full descriptions, illustrations, and sequence data are provided with interesting information as this species causes elliptical necrotic spots with a yellowish halo on living leaves of commercial oil palm plantations [,]. However, the type species was invalid because of the basionym lacked a Latin diagnosis []. From these, our fresh collection was collected from dead petiole of coconut (Cocos nucifera) and in phylogenetic analysis (Figure 1 and Figure 2), three strains of Hel. stilbacea, including our strain, are grouped together with high bootstrap support. In this study, we therefore provide a holotype from our specimen, and introduce a new species Helminthosporiella stilbacea, complete with an English diagnosis, and validated by using the same name while linking to the valuable information provided from the previous publication of this species.
A BLAST search of the ITS sequence of our isolate showed 90.19% similarity with H. velutinum (L131), the LSU sequence showed 97.05% similarity with H. aquaticum (MFLUCC 15-0357), the SSU sequence showed 99.15% similarity with H. quercinum (L90), and the tef1-α sequence showed 92.61% similarity with H. tiliae (L88). These blast results do not match the results of the phylogenetic analyses.
The comparison between three strains of Hel.stilbacea (see Table 4) from three collections showed that our collection MFLU 20-0521 has several differences when compared with the other two strains CPHmZC-01 and COAD 2126. Our collection was obtained from a dead petiole, while the two other strains were isolated from living leaves [,]. Therefore, our new collection has been provided as a holotype for Hel. Stilbacea. It is also the first geographical record from Thailand, and is a new record of the species from a coconut host (Cocos nucifera).
Table 4. Comparison of three strains of Helminthosporiella stilbacea.

4. Conclusions

In this study, we introduce the new genus Haplohelminthosporium,with Hap. calami as the type species. In multigene phylogenetic analyses, Hap.calami clustered together with Helminthosporium endiandrae (CBS 138902) without strong good bootstrap support (other H. endiandrae (AKRM1, CBS 138902 (ex-type), SM61) groups together in Helminthosporium). Moreover, we were unable to synonymize H. endiandrae (CBS 138902) under Haplohelminthosporium because H. endiandrae has only LSU sequence data available []. In the future, H. endiandrae needs more collections and sequence data to confirm taxonomic placement.
Another newly described isolate clusters together with Helminthosporiella stilbacea. Helminthosporiella was introduced by Crous et al. [] but was invalidated as the type species was not provided with a Latin diagnosis. In this study, we validate Helminthosporiella with Hel. stilbacea as the type species. Moreover, the newly described strain from this study is the first saprobic report of Hel. stilbacea, as this was reported in previous studies as a pathogenic fungus on leaves [,]. Moreover, topological nodes in phylogenic analyses showed conflicting results (Figure 1 and Figure 2). Probably, using only single gene ITS or LSU analyses will preclude the establishment of taxonomic placements, while combined gene analyses (including protein coding genes) provide sufficient molecular data to determine the placements.
Helminthosporium is generally described as a common saprobe found on leaf or twig litter, and it appears to have a diverse distribution. Occasionally, members of this genus are also described as pathogens, occurring on a wide range of hosts. Comparison of morphology is important for fungal identification []. In this study, we provide a checklist for Helminthosporium species reported worldwide including details of each species based on records from Species Fungorum [] (Table 5). We noted that ten Helminthosporium species have been found on palm substrates (Arecaceae). Although Helminthosporium conidia superficially resemble many genera, such as Drechslera, Bipolaris, and Exserohilum, phylogenetic analyses have provided different results [,,,,]. Furthermore, we recommend revision of the genus Helminthosporium with fresh collections and DNA sequence data (specifically the ITS region and protein coding genes).
Table 5. Morphology, host information, locality, sequence data, and related references of Helminthosporium reported worldwide based on the record of Species Fungorum 2021 (bold text present Helminthosporium reported from Arecaceae).

Author Contributions

Conceptualization, S.K., K.D.H., S.C.K., C.S. and S.T.; Data curation, S.K.; Methodology, S.K., A.M. and S.T.; Resources, K.D.H., S.C.K., J.X. and S.L.; Supervision, K.D.H. and S.T.; Writing—original draft, S.K., K.D.H., S.C.K., A.M., C.S., L.A.P.D., C.M.N., J.X. and S.T.; Writing—review & editing, S.K., K.D.H., S.C.K., S.T. and S.L. All authors have read and agreed to the published version of the manuscript.

Funding

Saowaluck Tibpromma would like to thank the International Postdoctoral Exchange Fellowship Program (number Y9180822S1), CAS President’s International Fellowship Initiative (PIFI) (number 2020PC0009), China Postdoctoral Science Foundation and the Yunnan Human Resources, and Social Security Department Foundation for funding her postdoctoral research. Kevin D. Hyde thanks the Thailand Research Funds for the grant “Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion (RDG6130001)”. Samantha Karunarathna thanks CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (number 2018PC0006) and the National Science Foundation of China (NSFC) for funding this research work under project code 31750110478. This work was partly supported by Chiang Mai University.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

Not applicable.

Acknowledgments

Sirinapa Konta is grateful to Paul Kirk, Shaun Pennycook, Jayarama Bhat, and Sirilak Radbouchoom, for their valuable suggestions and comments.

Conflicts of Interest

The authors declare no conflict of interest.

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