Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Proceedings of the National Academy of Sciences, Journal Year: 2012, Volume and Issue: 109(16), P. 6241 - 6246

Published: March 27, 2012

Six DNA regions were evaluated as potential barcodes for Fungi , the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region mitochondrial cytochrome c oxidase subunit 1 used animal barcode was excluded marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from nuclear ribosomal RNA cistron compared together with three representative protein-coding genes (largest polymerase II, minichromosome maintenance protein). Although gene had higher percent correct identification markers, low PCR amplification sequencing success eliminated them candidates universal fungal barcode. Among cistron, internal transcribed spacer (ITS) has highest probability successful broadest range most clearly defined gap between inter- intraspecific variation. subunit, popular phylogenetic marker certain groups, superior species resolution some taxonomic such early diverging lineages ascomycete yeasts, but otherwise slightly inferior ITS. small poor species-level fungi. ITS will formally proposed adoption primary Consortium Barcode Life, possibility that supplementary may developed particular narrowly circumscribed groups.

Language: Английский

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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

Fungal ecology, Journal Year: 2015, Volume and Issue: 20, P. 241 - 248

Published: July 22, 2015

Language: Английский

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Towards a unified paradigm for sequence‐based identification of fungi

Molecular Ecology, Journal Year: 2013, Volume and Issue: 22(21), P. 5271 - 5277

Published: Aug. 3, 2013

Abstract The nuclear ribosomal internal transcribed spacer ( ITS ) region is the formal fungal barcode and in most cases marker of choice for exploration diversity environmental samples. Two problems are particularly acute pursuit satisfactory taxonomic assignment newly generated sequences: (i) lack an inclusive, reliable public reference data set (ii) means to refer species, which no Latin name available a standardized stable way. Here, we report on progress these regards through further development UNITE database http://unite.ut.ee molecular identification fungi. All species represented by at least two sequences international nucleotide sequence databases now given unique, accession number type (e.g. H ymenoscyphus pseudoalbidus | GU 586904| SH 133781.05 FU ), their ecological annotations were corrected as far possible distributed, third‐party annotation effort. We introduce term ‘species hypothesis’ taxa discovered clustering different similarity thresholds (97–99%). An automatically or manually designated chosen represent each such SH. These released http://unite.ut.ee/repository.php use scientific community in, example, local searches QIIME pipeline. system will be updated grows. invite everybody position improve metadata associated with particular lineages expertise do so new Web‐based management .

Language: Английский

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Global diversity and geography of soil fungi

Science, Journal Year: 2014, Volume and Issue: 346(6213)

Published: Nov. 28, 2014

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds globally distributed soil samples, we demonstrate that richness is decoupled plant diversity. The plant-to-fungus ratio declines exponentially toward poles. Climatic factors, followed by edaphic spatial variables, constitute best predictors community composition at global scale. show similar latitudinal gradients to other organisms, with several notable exceptions. These findings advance our understanding permit integration fungi into a general macroecological framework.

Language: Английский

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Mycorrhizal ecology and evolution: the past, the present, and the future

New Phytologist, Journal Year: 2015, Volume and Issue: 205(4), P. 1406 - 1423

Published: Feb. 2, 2015

Summary Almost all land plants form symbiotic associations with mycorrhizal fungi. These below‐ground fungi play a key role in terrestrial ecosystems as they regulate nutrient and carbon cycles, influence soil structure ecosystem multifunctionality. Up to 80% of plant N P is provided by many species depend on these symbionts for growth survival. Estimates suggest that there are c . 50 000 fungal 250 species. The development high‐throughput molecular tools has helped us better understand the biology, evolution, biodiversity associations. Nuclear genome assemblies gene annotations 33 now available providing fascinating opportunities deepen our understanding lifestyle, metabolic capabilities symbionts, dialogue between evolutionary adaptations across range Large‐scale surveys have novel insights into diversity, spatial temporal dynamics communities. At ecological level, network theory makes it possible analyze interactions plant–fungal partners complex underground multi‐species networks. Our analysis suggests nestedness, modularity specificity networks vary type. Mechanistic models explaining partner choice, resource exchange, coevolution been developed being tested. This review ends major frontiers further research. Contents 1406 I. Introduction 1407 II. Biodiversity 1408 III. Carbon cycling multifunctionality 1410 IV. Mycorrhizal 1411 V. Evolution selection 1413 VI. genomics crosstalk 1416 VII. Conclusions future research 1418 Acknowledgements References 1419

Language: Английский

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MycoCosm portal: gearing up for 1000 fungal genomes

Nucleic Acids Research, Journal Year: 2013, Volume and Issue: 42(D1), P. D699 - D704

Published: Dec. 1, 2013

MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination genome sequences other 'omics' data providing interactive web-based tools. also promotes facilitates user community participation through nomination new species fungi for sequencing, annotation resulting data. By efficiently filling gaps in Fungal Tree Life, will help address important problems associated with energy environment, taking advantage growing resources.

Language: Английский

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One Juliet and four Romeos: VeA and its methyltransferases

Frontiers in Microbiology, Journal Year: 2015, Volume and Issue: 6

Published: Jan. 20, 2015

Fungal secondary metabolism has become an important research topic with great biomedical and biotechnological value. In the postgenomic era, understanding diversity molecular control of metabolites (SMs) are two challenging tasks addressed by community. Discovery LaeA methyltransferase 10 years ago opened up a new horizon on SM when it was found that expression many gene clusters is controlled LaeA. While function remains enigma, discovery velvet family proteins as interaction partners further extended role beyond metabolism. The heterotrimeric VelB-VeA-LaeA complex plays roles in development, sporulation, metabolism, pathogenicity. Recently, three other methyltransferases have been to associate complex, LaeA-like F heterodimers VipC-VapB. Interaction VeA at least four indicates hub for questions: Is there supercomplex or part highly dynamic cellular network different partners?

Language: Английский

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Fungal Diversity Revisited: 2.2 to 3.8 Million Species

Microbiology Spectrum, Journal Year: 2017, Volume and Issue: 5(4)

Published: July 28, 2017

The question of how many species Fungi there are has occasioned much speculation, with figures mostly posited from around half a million to 10 million, and in one extreme case even sizable portion the spectacular number 1 trillion. Here we examine new evidence various sources derive an updated estimate global fungal diversity. rates patterns description 1750s show no sign approaching asymptote accelerated 2010s after advent molecular approaches delimitation. Species recognition studies (semi-)cryptic hidden morpho-species complexes suggest weighted average ratio about order magnitude for recognized before such studies. New also comes extrapolations plant:fungus ratios, information now being generated environmental sequence studies, including comparisons fieldwork data same sites. We further draw attention undescribed awaiting discovery biodiversity hot spots tropics, little-explored habitats (such as lichen-inhabiting fungi), material collections study. conclude that commonly cited 1.5 is conservative actual range properly estimated at 2.2 3.8 million. With 120,000 currently accepted species, it appears best just 8%, worst scenario 3%, named so far. Improved estimates hinge particularly on reliable statistical phylogenetic analyze rapidly increasing amount data.

Language: Английский

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The gut mycobiome of the Human Microbiome Project healthy cohort

Microbiome, Journal Year: 2017, Volume and Issue: 5(1)

Published: Nov. 25, 2017

Most studies describing the human gut microbiome in healthy and diseased states have emphasized bacterial component, but fungal (i.e., mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, mycobiome primarily been disease centric or small cohorts individuals. contribute existing knowledge mycobiome, we investigated Human Microbiome Project (HMP) cohort by sequencing Internal Transcribed Spacer 2 (ITS2) region well 18S rRNA gene.Three hundred seventeen HMP stool samples were analyzed ITS2 sequencing. Fecal diversity was significantly lower comparison diversity. Yeast dominated samples, comprising eight top 15 most abundant genera. Specifically, communities characterized high prevalence Saccharomyces, Malassezia, Candida, with S. cerevisiae, M. restricta, C. albicans operational taxonomic units (OTUs) present 96.8, 88.3, 80.8% respectively. There degree inter- intra-volunteer variability communities. However, OTUs found 92.2, 78.3, 63.6% volunteers, respectively, all donated over an approximately 1-year period. Metagenomic gene data agreed results; however, provided greater resolution relatively low abundance constituents.Compared communities, yeast including Candida. Both high, revealing that unlike individual's no more similar itself time than another person's. Nonetheless, several species persisted across majority evidence core may exist. membership compared metagenomic data, suggesting it sensitive method for studying samples.

Language: Английский

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Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community

Journal of Natural Products, Journal Year: 2017, Volume and Issue: 80(3), P. 756 - 770

Published: Feb. 15, 2017

Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, pharmaceutical applications. Despite importance chemistry, identification fungi remains a daunting task chemists, especially those who do not work trained mycologist. The purpose this review is update about the tools available molecular fungi. In particular, we discuss (1) problems using morphology alone species level; (2) three nuclear ribosomal genes most commonly used fungal potential advantages limitations ITS region, official DNA barcoding marker species-level fungi; (3) how use NCBI-BLAST search barcoding, cautionary note regarding its limitations; (4) curated databases containing sequences; (5) various protein-coding augment or supplant certain groups; (6) methods construction phylogenetic trees from sequences facilitate identification. We recommend that, whenever possible, both data be Our goal that will provide set standardized procedures can utilized by research community.

Language: Английский

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