Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi

Mycology&#58 An International Journal on Fungal Biology, Journal Year: 2019, Volume and Issue: 10(3), P. 127 - 140

Published: May 7, 2019

The global bio-diversity of fungi has been extensively investigated and their species number estimated. Notably, the development molecular phylogeny revealed an unexpected fungal diversity utilisation culture-independent approaches including high-throughput amplicon sequencing dramatically increased operational taxonomic units. A novel taxa new divisions, classes, orders families have established in last decade. Many cryptic were identified by phylogeny. Based on recently generated data from culture-dependent -independent survey same samples, earth estimated to be 12 (11.7–13.2) million compared 2.2–3.8 a variety estimation techniques. Moreover, it speculated that current use techniques would reveal even higher than our estimation. Recently, formal classification environmental sequences permission DNA sequence as names' type proposed but strongly objected mycologist community. Surveys unusual niches indicated many previously regarded "unculturable fungi" could cultured certain substrates under specific conditions. sequencing, shotgun metagenomics single-cell genomics powerful means detect taxa. Here, we propose separate types into physical based specimen, genome (gDNA) complete culturable uncluturable specimen digital data. gDNA should priority, while can temporal supplementary before being available. name "digital type" assigned "clade" + name. genus, family or order, etc. which affiliates to. Facilitating future cultivation efforts encouraged. Also, with advancement knowledge inhabiting various environments mostly because rapid detection technologies, more information expected for planet.

Language: Английский

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A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes

IMA Fungus, Journal Year: 2019, Volume and Issue: 10(1)

Published: June 7, 2019

Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic aero-aquatic hyphomycetes, mammalian saprobes. These fungi commonly detected cultures from diseased tissue environmental DNA extracts. The identification specimens such character-poor samples increasingly relies on sequencing. However, current classification is still largely based morphologically defined taxa, especially at higher taxonomic levels. Consequently, formal frequently poorly congruent with relationships suggested by sequencing studies. Previous class-wide phylogenies have been ribosomal markers, most published multi-gene studies being focussed particular genera or families. In this paper we collate data available representing both sexual asexual morphs across genetic breadth class, a focus generic type species, to present phylogeny up 15 concatenated genes 279 specimens. Included dataset that were extracted 72 genomes for 10 new released study. To test statistical support deepest branches phylogeny, an additional 3156 51 selected also presented. fill some gaps 15-gene further ITS gene tree, particularly targeting ex-type species. A small number novel taxa proposed: Marthamycetales ord. nov., Drepanopezizaceae Mniaeciaceae fams. nov. changes limited part because ad hoc nature taxon specimen selection, purely availability data. constitutes framework enabling future taxonomically targeted using deliberate selection. Such will ideally include designation epitypes species those which not able be original specimen, consideration morphological characters whenever genetically clades recognized as within classification.

Language: Английский

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Ganoderma lingzhi (Polyporales, Basidiomycota): the scientific binomial for the widely cultivated medicinal fungus Lingzhi

Mycological Progress, Journal Year: 2017, Volume and Issue: 16(11-12), P. 1051 - 1055

Published: Oct. 23, 2017

Language: Английский

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Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal “from the floor” to allow DNA sequences as types of names

IMA Fungus, Journal Year: 2018, Volume and Issue: 9(1), P. 185 - 198

Published: June 1, 2018

We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus 9: 167–175, 2018) and Thines 177–183, 2018). While we agree with some the principal arguments brought forward these authors, address misconceptions demonstrate that presumed evidence presented in has been wrongly interpreted. disagree allowing sequences as types would fundamentally alter nature types, since a similar abstracted features type is already allowed Code (Art. 40.5), an illustration. also there high risk introducing artifactual taxa, this can be quantified at well below 5 %, considering various high-throughput sequencing errors. Contrary apparently widespread misconceptions, nomenclature cannot based on similarity-derived OTUs their consensus sequences, but must derived from rigorous, multiple alignment-based phylogenetic methods quantitative, single-marker species recognition algorithms, using original sequence reads; it therefore identical its approach studies physical Code. recognize limitations ITS single fungal barcoding marker, point out result conservative approach, 'false negatives" surpassing "false positives"; desirable feature nomenclature. Sequence-based does not aim accurately resolving species, naming represent unknown lineages so serve means communication, ending untenable situation exponentially growing number unlabeled fill online repositories. The risks are outweighed gains obtained reference library named spanning full array diversity. Finally, elaborate provisions addition our proposal amend take care issues approach. In particular, taking up idea Candidatus status invalid, provisional names prokaryote propose compromise allow valid publication voucherless, consistent manner, obligate designation "nom. seq." (nomen sequentiae). Such have priority over specimen- or culture-based unless either epitypified adopted for protection recommendation committee International Commission Taxonomy Fungi following evaluation strict quality control underlying established rules recommendations.

Language: Английский

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Verrucoccum (Dothideomycetes, Dictyosporiaceae), a new genus of lichenicolous fungi on Lobaria s. lat. for the Dothidea hymeniicola species complex

Mycologia, Journal Year: 2021, Volume and Issue: unknown, P. 1 - 20

Published: Sept. 30, 2021

Two lichenicolous fungi, one growing on the thallus of Lobaria pulmonaria in United Kingdom (Scotland) and other apothecia linita L. oregana northwestern North America (Alaska British Columbia) northeast Asia (Russian Far East, Khabarovsk Krai), show similarities to species originally described as Dothidea hymeniicola (later transferred Polycoccum s. lat Endococcus) from a lat. Central America. Critical morphological comparison showed that, despite superficial resemblance between Alaskan, Canadian, Russian, Scottish collections holotype hymeniicola, they can be distinguished by detailed microscopic analyses. Using three molecular markers, sequences nuc 18S, 28S, internal transcribed spacer (ITS) rDNA regions recent Alaskan were obtained. Phylogenetic analyses confirmed separation revealed them new lineage Pleosporales, for which generic name Verrucoccum is introduced species: V. coppinsii, sp. nov., comb. nov. (syn. hymeniicola), spribillei,

Language: Английский

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News

IMA Fungus, Journal Year: 2018, Volume and Issue: 9(2), P. A47 - A51

Published: Dec. 1, 2018

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