Nomenclatural and identification pitfalls of endophytic mycota based on DNA sequence analyses of ribosomal and protein genes phylogenetic markers: A taxonomic dead end?

Jeewon, Rajesh

doi:10.5943/mycosphere/8/10/7

Cited by 25 publications

(12 citation statements)

References 17 publications

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“…PCR amplifications were conducted as outlined by Jeewon et al . 38,39 and PCR products were sequenced by GenScript Biotechnology Co., Nanjing, China.…”

Section: Methodsmentioning

confidence: 99%

Multigene phylogenetics of Polycephalomyces (Ophiocordycipitaceae, Hypocreales), with two new species from Thailand

Xiao

Wen

Hongsanan

et al. 2018

Sci Rep

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Polycephalomyces (Ophiocordycipitaceae) species are found in subtropical regions and are parasitic or hyperparasitic on insects. Two new species, P. aurantiacus and P. marginaliradians, parasitic on Ophiocordyceps barnesii and larva of Cossidae respectively, are introduced in this paper. Morphological comparison with extant species and DNA based phylogenies from analyses of a multigene dataset support the establishment of the new taxa. Polycephalomyces aurantiacus, exhibiting a hyperparasitic lifestyle on Ophiocordyceps barnesii, differs from other species in producing orange conidia in mass and have longer β-phialides in culture. Polycephalomyces marginaliradians differs from other Ophiocordyceps species by producing single stromata with a stipe, smaller perithecia and branched α-phialides and catenate α-conidia and is parasitic on Cossidae. A combined nrSSU, nrLSU, ITS, tef-1a, rpb1 and rpb2 sequence data was analysed phylogenetically including Ophiocordyceps and Polycephalomyces taxa. The new species described herein are clearly distinct from other species in Polycephalomyces. We provide a key to the species of Polycephalomyces and discuss relevant interspecies relationships.

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“…PCR amplifications were conducted as outlined by Jeewon et al . 38,39 and PCR products were sequenced by GenScript Biotechnology Co., Nanjing, China.…”

Section: Methodsmentioning

confidence: 99%

Multigene phylogenetics of Polycephalomyces (Ophiocordycipitaceae, Hypocreales), with two new species from Thailand

Xiao

Wen

Hongsanan

et al. 2018

Sci Rep

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“…Jeewon et al 2003Jeewon et al , 2017Ariyawansa et al 2015;Liu et al 2015;Hyde et al 2017a, b;Tibpromma et al 2017;Wanasinghe et al 2017Wanasinghe et al , 2018Jayawardena et al 2018a, b). The use of other molecular approaches based on DNA sequence data (e.g.…”

Section: Using Mgdna From Environment In Species Identificationmentioning

confidence: 99%

Can we use environmental DNA as holotypes?

et al. 2018

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The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (''mgDNA'') from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these 'dark taxa' or 'dark matter fungi' that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

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“…There is a need to translate those molecular sequences into formal taxonomic names and consider them nomenclaturally valid to facilitate taxonomy, as postulated by Hibbett 50 and Jeewon et al . 51 but with caution 52 .…”

Section: Discussionmentioning

confidence: 99%

Hidden mycota of pine needles: Molecular signatures from PCR-DGGE and Ribosomal DNA phylogenetic characterization of novel phylotypes

Jeewon

Yeung

Wannasinghe

et al. 2018

Sci Rep

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Previous studies for enumerating fungal communities on pine needles relied entirely on phenotypic diversity (microscopy) or identification based on DNA sequence data from those taxa recovered via cultural studies. To bypass limitations of the culturing methods and provide a more realistic diversity estimate, we employed and assessed a PCR-DGGE based method coupled with rDNA phylogenetic sequence analyses to characterize fungal taxa associated with pine needles. Fresh (living) and decayed needles from three hosts of the Pinaceae (Keteleeria fortunei, Pinus elliottii and P. massoniana) were examined. Morphological studies reveal that the most abundant species associated with decayed needles were Cladosporium cladosporioides and an unidentified Trichoderma species followed by Gliocephalotrichum sp., Gliocladium sp., Lophodermium pinastri, Paecilomyces varioti, Phaeostalagmus cyclosporus and a Phoma sp, which are commonly occurring fungi. Community genomic data from freshly collected and decayed pine needles recovered 40 operational taxonomic units, which appear to be mostly undetected members of the natural fungal consortium. Sequence analyses revealed a number of phylotypes or “species” that were not recovered using traditional morphological and cultural approaches previously used. Phylogenetic data from partial 18S rDNA sequence data reveal that most phylotypes represent potential novel phylogenetic fungal lineages with affinities to the Dothideomycetes, Leotiomycetes, Lecanoromycetes and Sordariomycetes and were not identical to previously known endophytes or saprobes. Although the major ecological roles of these phylotypes in pine needles are still enigmatic, this study provides new insights in hidden fungal diversity that mycologists are possibly ignoring given the discrepancies associated with available methods. To what extent do previously recovered identified species (either as saprobes or endophytes) from morphological or culturing studies act as pioneer decomposers or constitute an integral part of endophytic community warrants further investigation.

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Nomenclatural and identification pitfalls of endophytic mycota based on DNA sequence analyses of ribosomal and protein genes phylogenetic markers: A taxonomic dead end?

Cited by 25 publications

References 17 publications

Multigene phylogenetics of Polycephalomyces (Ophiocordycipitaceae, Hypocreales), with two new species from Thailand

Multigene phylogenetics of Polycephalomyces (Ophiocordycipitaceae, Hypocreales), with two new species from Thailand

Can we use environmental DNA as holotypes?

Hidden mycota of pine needles: Molecular signatures from PCR-DGGE and Ribosomal DNA phylogenetic characterization of novel phylotypes

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