The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D259 - D264

Published: Oct. 12, 2018

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 public ITS sequences reference. These are clustered into ∼459 species hypotheses assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house third-party curation annotation have resulted in more than 275 improvements data over past 15 years. serves as provider range metabarcoding software pipelines regularly exchanges with major databases other community resources. Recent include redesigned handling unclassifiable hypotheses, integration taxonomic backbone Global Biodiversity Information Facility, support an unlimited number parallel classification systems.

Language: Английский

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Mycobiome diversity: high-throughput sequencing and identification of fungi

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 17(2), P. 95 - 109

Published: Nov. 15, 2018

Language: Английский

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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 10, 2020

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of based on global richness estimates, with around 3 million predicted species. Compared to plants animals, have simple body plans often morphologically ecologically obscure structures. This poses challenges for accurate precise identifications. Here we provide a conceptual framework identification fungi, encouraging approach integrative (polyphasic) taxonomy species delimitation, i.e. combination genealogy (phylogeny), phenotype (including autecology), reproductive biology (when feasible). allows objective evaluation diagnostic characters, either phenotypic or molecular both. Verification identifications is crucial but neglected. Because clade-specific evolutionary histories, there currently no single tool although DNA barcoding using internal transcribed spacer (ITS) remains first diagnosis, particularly in metabarcoding studies. Secondary barcodes are increasingly implemented groups where ITS does not sufficient precision. Issues pairwise sequence similarity-based OTU clustering discussed, multiple alignment-based phylogenetic approaches subsequent verification recommended as more alternatives. In approaches, trade-off between speed accuracy precision must be carefully considered. Intragenomic variation other markers should properly documented, phylotype diversity necessarily proxy richness. Important strategies improve are: (1) broadly document intraspecific intragenomic markers; (2) substantially expand repositories, focusing undersampled clades missing taxa; (3) curation labels primary repositories increase number sequences verified material; (4) link data digital information voucher specimens including imagery. parallel, technological improvements genome sequencing offer promising alternatives future. Despite prevalence DNA-based fungal taxonomy, phenotype-based remain an important strategy catalog establish initial hypotheses.

Language: Английский

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New scientific discoveries: Plants and fungi

Plants People Planet, Journal Year: 2020, Volume and Issue: 2(5), P. 371 - 388

Published: Sept. 1, 2020

Societal Impact Statement Research and publication of the planet's remaining plant fungal species as yet unknown to science is essential if we are address United Nations Sustainable Development Goal (SDG) 15 “Life on Land” which includes protection terrestrial ecosystems halting biodiversity loss. If not known science, they cannot be assessed International Union for Conservation Nature (IUCN) Red List Threatened Species so possibility protect them from extinction reduced. Furthermore, until fully scientifically evaluated their potential new foods, medicines, products would help SDGs 1,2,3, 8. Summary Scientific discovery, including naming taxa, important because without a scientific name, invisible possibilities researching its ecology, applications threats, conserving it, greatly We review discoveries in kingdoms, based largely names taxa published 2019 indexed Plant Names Index Fungorum. Numbers both kingdoms were similar with 1942 1882 fungi. However, while >50% have likely been discovered, >90% fungi remain unknown. This gulf explains greater number higher order 2019: three classes, 18 orders, 48 families 214 genera versus one family 87 plants. compare terms rates globally different taxonomic groups geographic areas, regard use DNA discovery. especially those interest humanity products, also by life‐form. consider where future such can expected. recommend an urgent increase investment discovery species, still survive. Priorities include more training taxonomists, building equipping collections‐based research centers them, species‐rich, income‐poor countries bulk thought occur.

Language: Английский

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Toward a Fully Resolved Fungal Tree of Life

Annual Review of Microbiology, Journal Year: 2020, Volume and Issue: 74(1), P. 291 - 313

Published: July 14, 2020

In this review, we discuss the current status and future challenges for fully elucidating fungal tree of life. last 15 years, advances in genomic technologies have revolutionized systematics, ushering field into phylogenomic era. This has made unthinkable possible, namely access to entire genetic record all known extant taxa. We first review highlight areas where additional effort will be required. then analytical imposed by volume data methods recover most accurate species given sea gene trees. Highly resolved deeply sampled trees are being leveraged novel ways study radiations, delimitation, metabolic evolution. Finally, critical issue incorporating unnamed uncultured dark matter taxa that represent vast majority diversity.

Language: Английский

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101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens

Studies in Mycology, Journal Year: 2020, Volume and Issue: 96, P. 141 - 153

Published: Feb. 1, 2020

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity lifestyles, many which have evolved multiple times. Plant pathogens represent a major ecological niche they are known to infect most food crops feedstocks for biomass biofuel production. Studying ecology evolution has significant implications our fundamental understanding fungal evolution, their adaptation stress host specificity, practical with regard effects climate change on food, feed, livestock elements agro-economy. In this study, we present first large-scale, whole-genome comparison 101 introducing 55 newly sequenced species. The availability data produced high-confidence phylogeny leading reclassification 25 organisms, provided clearer picture relationships among various families, indicated that pathogenicity times within class. We also identified gene family expansions contractions across linked niches providing insights into genome group. Using machine-learning methods classified fungi lifestyle classes >95 % accuracy small number families positively correlated these distinctions. This can become valuable tool genome-based prediction species lifestyle, especially rarely seen poorly studied

Language: Английский

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The numbers of fungi: is the descriptive curve flattening?

Fungal Diversity, Journal Year: 2020, Volume and Issue: 103(1), P. 219 - 271

Published: July 1, 2020

Language: Английский

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Fungal taxonomy and sequence-based nomenclature

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(5), P. 540 - 548

Published: April 26, 2021

Language: Английский

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Integrative approaches for species delimitation in Ascomycota

Fungal Diversity, Journal Year: 2021, Volume and Issue: 109(1), P. 155 - 179

Published: July 1, 2021

Language: Английский

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The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding

Fungal Diversity, Journal Year: 2022, Volume and Issue: 114(1), P. 327 - 386

Published: April 28, 2022

Abstract The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million species, but the number formally described taxa around 150,000, a tiny fraction total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new each genus. To highlight importance traditional morpho-molecular methods publishing novel that are considered have low discovery. We discuss whether likely be rare or due lack extensive sampling classification. Apiospora , Bambusicola Beltrania Capronia Distoseptispora Endocalyx Neocatenulostroma Neodeightonia Paraconiothyrium Peroneutypa Phaeoacremonium Vanakripa . host-specificity selected compare epithets genus with ITS (barcode) sequences deposited GenBank UNITE. furthermore relationship divergence times these those their hosts. hypothesize there might more hosts habitats should investigated for

Language: Английский

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