51
|
Yahr R, Schoch CL, Dentinger BTM. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150336. [PMID: 27481788 PMCID: PMC4971188 DOI: 10.1098/rstb.2015.0336] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 11/15/2022] Open
Abstract
The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'.
Collapse
Affiliation(s)
- Rebecca Yahr
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Bryn T M Dentinger
- Royal Botanic Gardens Kew, Richmond, Surrey, UK Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Cledwyn Building, Penglais, Aberystwyth SY23 3DD, UK
| |
Collapse
|
52
|
Abstract
Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.
Collapse
Affiliation(s)
- Jianping Xu
- a Department of Biology, McMaster University, Hamilton, ON, Canada.,b Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan, PR China.,c Institute of Tropical Diseases, Hainan Medical University, Haikou, Hainan, PR China
| |
Collapse
|
53
|
Redhead SA, Vizzini A, Drehmel DC, Contu M. Saproamanita, a new name for both Lepidella E.-J. Gilbert and Aspidella E.-J. Gilbert (Amaniteae, Amanitaceae). IMA Fungus 2016; 7:119-29. [PMID: 27433443 PMCID: PMC4941681 DOI: 10.5598/imafungus.2016.07.01.07] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/17/2016] [Indexed: 01/23/2023] Open
Abstract
The genus Amanita has been divided into two monophyletic taxa, Amanita, an ectomycorrhizal genus, and Aspidella, a saprotrophic genus. The controversies and histories about recognition of the two genera based on trophic status are discussed. The name Aspidella E.-J. Gilbert is shown to be illegitimate and a later homonym of Aspidella E. Billings, a well-known generic name for an enigmatic fossil sometimes classified as a fungus or alga. The name Saproamanita is coined to replace Aspidella E.-J. Gilbert for the saprotrophic Amanitas, and a selection of previously molecularly analyzed species and closely classified grassland species are transferred to it along with selected similar taxa. The type illustration for the type species, S. vittadinii, is explained and a subgeneric classification accepting Amanita subgen. Amanitina and subgen. Amanita is proposed. Validation of the family name, Amanitaceae E.-J. Gilbert dating from 1940, rather than by Pouzar in 1983 is explained.
Collapse
Affiliation(s)
- Scott A Redhead
- National Mycological Herbarium of Canada, Central Experimental Farm, Ottawa Research & Development Centre, Science & Technology Branch, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Alfredo Vizzini
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125 Torino, Italy
| | | | | |
Collapse
|
54
|
Díaz-Valderrama JR, Aime MC. The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally. Heredity (Edinb) 2016; 116:491-501. [PMID: 26932308 PMCID: PMC4868271 DOI: 10.1038/hdy.2016.5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/25/2015] [Indexed: 01/22/2023] Open
Abstract
The cacao pathogen Moniliophthora roreri belongs to the mushroom-forming family Marasmiaceae, but it has never been observed to produce a fruiting body, which calls to question its capacity for sexual reproduction. In this study, we identified potential A (HD1 and HD2) and B (pheromone precursors and pheromone receptors) mating genes in M. roreri. A PCR-based method was subsequently devised to determine the mating type for a set of 47 isolates from across the geographic range of the fungus. We developed and generated an 11-marker microsatellite set and conducted association and linkage disequilibrium (standardized index of association, IA(s)) analyses. We also performed an ancestral reconstruction analysis to show that the ancestor of M. roreri is predicted to be heterothallic and tetrapolar, which together with sliding window analyses support that the A and B mating loci are likely unlinked and follow a tetrapolar organization within the genome. The A locus is composed of a pair of HD1 and HD2 genes, whereas the B locus consists of a paired pheromone precursor, Mr_Ph4, and receptor, STE3_Mr4. Two A and B alleles but only two mating types were identified. Association analyses divided isolates into two well-defined genetically distinct groups that correlate with their mating type; IA(s) values show high linkage disequilibrium as is expected in clonal reproduction. Interestingly, both mating types were found in South American isolates but only one mating type was found in Central American isolates, supporting a prior hypothesis of clonal dissemination throughout Central America after a single or very few introductions of the fungus from South America.
Collapse
Affiliation(s)
- J R Díaz-Valderrama
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - M C Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
55
|
Thiéry O, Vasar M, Jairus T, Davison J, Roux C, Kivistik PA, Metspalu A, Milani L, Saks Ü, Moora M, Zobel M, Öpik M. Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions ofRhizophagus irregularisandGigaspora margaritais high and isolate-dependent. Mol Ecol 2016; 25:2816-32. [DOI: 10.1111/mec.13655] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/29/2016] [Accepted: 04/14/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Odile Thiéry
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Martti Vasar
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Teele Jairus
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - John Davison
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales; UPS; CNRS 24 chemin de Borde Rouge-Auzeville; BP 42617; Université de Toulouse; 31326 Castanet-Tolosan France
| | - Paula-Ann Kivistik
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Andres Metspalu
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Lili Milani
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Ülle Saks
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Mari Moora
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Martin Zobel
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Maarja Öpik
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| |
Collapse
|
56
|
Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M. Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 2016. [DOI: 10.3897/mycokeys.13.8140] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|
57
|
The cacao pathogen Moniliophthora roreri (Marasmiaceae) produces rhexolytic thallic conidia and their size is influenced by nuclear condition. MYCOSCIENCE 2016. [DOI: 10.1016/j.myc.2016.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
58
|
Affiliation(s)
- Sven Buerki
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | | |
Collapse
|
59
|
The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts. FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-015-0351-8] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
60
|
Yoshida K, Sasaki E, Kamoun S. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:771. [PMID: 26442080 PMCID: PMC4585160 DOI: 10.3389/fpls.2015.00771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/07/2015] [Indexed: 05/20/2023]
Abstract
The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.
Collapse
Affiliation(s)
- Kentaro Yoshida
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe UniversityKobe, Japan
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
- *Correspondence: Kentaro Yoshida, Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-Ku, Kobe, Japan,
| | - Eriko Sasaki
- Gregor Mendel Institute, Austrian Academy of Sciences, ViennaAustria
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
| |
Collapse
|