Fungal DNA barcoding

Genome ◽  
2016 ◽  
Vol 59 (11) ◽  
pp. 913-932 ◽  
Author(s):  
Jianping Xu
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Species Recognition ◽  
Its Region ◽  
Ecosystem Functions ◽  
Future Research ◽  
Reference Database ◽  
Identification System ◽  
Spatial And Temporal Patterns ◽  
Fungal Dna

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.

scholarly journals Database establishment for the secondary fungal DNA barcodetranslational elongation factor 1α(TEF1α)

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 160-169 ◽  
Author(s):  
Wieland Meyer ◽  
Laszlo Irinyi ◽  
Minh Thuy Vi Hoang ◽  
Vincent Robert ◽  
Dea Garcia-Hermoso ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Fungal Infections ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Its Region ◽  
Reference Sequence ◽  
Diagnostic Tools ◽  
Reference Database ◽  
Elongation Factor 1Α ◽  
Fungal Dna

With new or emerging fungal infections, human and animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but it has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode that together with the ISHAM-ITS database, forms the ISHAM barcode database, available online at http://its.mycologylab.org/ . We encourage the mycology community for active contributions.

DNA barcoding for wood identification: global review of the last decade and future perspective

IAWA Journal ◽  
2020 ◽  
Vol 41 (4) ◽  
pp. 620-643 ◽  
Author(s):  
Lichao Jiao ◽  
Yang Lu ◽  
Tuo He ◽  
Juan Guo ◽  
Yafang Yin
Keyword(s):  
Dna Barcoding ◽  
Extraction Methods ◽  
Future Perspective ◽  
Future Research ◽  
Reference Database ◽  
Wood Identification ◽  
Accurate Identification ◽  
Research Orientation ◽  
Timber Trade ◽  
Dna Extraction Methods

Abstract DNA barcoding technology has emerged as one of the most promising tools available to identify timber at the species level, contributing to the monitoring of the timber trade and the conservation of forestry sources. This paper reviews the progress, challenges, and existing problems in the development of DNA barcoding for wood identification in the last ten years. There is a focus on the optimization of DNA extraction methods for processed or ancient wood, the strategy of screening high-resolution DNA barcodes suitable for wood identification, the development of a wood DNA reference database especially for priority taxa, and the comparison and comprehensive application of sequence analytical methods to achieve accurate identification. In addition to DNA barcoding, the feasibility of other genetic methods for wood identification is also discussed. Furthermore, future research orientation and strategy of wood DNA barcoding are presented. We argue that wood DNA barcoding integrated with other methodologies including wood anatomy can offer an effective approach and a new perspective to promote legal logging for timber trade custody and global biodiversity conservation.

Sequence-based Identification and Classification of Fungi.

2021 ◽  
pp. 198-216
Author(s):  
Andrew M. Borman ◽  
Elizabeth M. Johnson
Keyword(s):  
Dna Sequences ◽  
Its Region ◽  
Pcr Primers ◽  
Taxonomic Resolution ◽  
Its2 Region ◽  
Rrna Gene ◽  
5.8S Rrna Gene ◽  
Fungal Identification ◽  
Identification Of Fungi ◽  
Fungal Dna

Abstract This book chapter describes the advantages and limitations of the ITS Region as a universal barcode for fungal identification. The ITS region offers several practical advantages as a universal fungal barcode region. The region encompasses segments that permit resolution at different taxonomic levels as it includes the highly conserved 5.8S rRNA gene, the moderately rapidly evolving ITS2 region and the rapidly evolving ITS1 region, flanked by the highly conserved SSU and LSU genes which permit design of PCR primers that are almost panfungal. Over the last two decades the sequence-based identification of fungi has certainly come of age. The ITS region is universally accepted as the primary fungal barcoding region owing to the high barcode gap with the locus for many groups of fungi. Since the species-resolution power of ITS is poor for certain groups of fungi, and higher-level taxonomic resolution is greater with proteincoding genes, the TEF1α locus has been proposed as the universal secondary barcode region. In addition, the historical problems surrounding the reliability of fungal DNA sequences in centralized repositories are slowly being resolved by the development of an increasing number of publicly accessible, curated databases.

scholarly journals Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

2016 ◽  
Author(s):  
Panu Somervuo ◽  
Douglas Yu ◽  
Charles Xu ◽  
Yinqiu Ji ◽  
Jenni Hultman ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Environmental Data ◽  
Reference Sequence ◽  
Future Research ◽  
List Type ◽  
Reference Databases ◽  
Sequence Databases ◽  
Taxonomic Groups

AbstractA crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference databases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability.In this paper we evaluate the performance of a recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals, and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (from 800 to 130 000 species), and variation in the completeness of the reference databases (representing 15% to 100% of the species).Our results demonstrate that PROTAX yields essentially unbiased assessment of probabilities of taxonomic placement, and thus that its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence databases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels.Our results show that reliable species-level identification from environmental samples is still challenging, and thus neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion and pruning of taxonomic and reference sequence databases, and making these two types of data compatible.

Old-growth forest reserves in Slovenia: the past, present, and future

2012 ◽  
Vol 163 (6) ◽  
pp. 240-246 ◽  
Author(s):  
Thomas A. Nagel ◽  
Jurij Diaci ◽  
Dusan Rozenbergar ◽  
Tihomir Rugani ◽  
Dejan Firm
Keyword(s):  
Stand Structure ◽  
Growth Conditions ◽  
Ecosystem Functions ◽  
Future Research ◽  
Old Growth ◽  
Forest Reserves ◽  
The Past ◽  
Old Growth Forest ◽  
Forest Remnants ◽  
Basic Characteristics

Old-growth forest reserves in Slovenia: the past, present, and future Slovenia has a small number of old-growth forest remnants, as well as many forest reserves approaching old-growth conditions. In this paper, we describe some of the basic characteristics of these old-growth remnants and the history of their protection in Slovenia. We then trace the long-term development of research in these old-growth remnants, with a focus on methodological changes. We also review some of the recent findings from old-growth research in Slovenia and discuss future research needs. The conceptual understanding of how these forests work has slowly evolved, from thinking of them in terms of stable systems to more dynamic and unpredictable ones due to the influence of natural disturbances and indirect human influences. In accordance with this thinking, the methods used to study old-growth forests have changed from descriptions of stand structure to studies that address natural processes and ecosystem functions.

scholarly journals Morpho-molecular identification and first report of Fusarium equiseti in causing chilli wilt from Kashmir (Northern Himalayas)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ammarah Hami ◽  
Rovidha S. Rasool ◽  
Nisar A. Khan ◽  
Sheikh Mansoor ◽  
Mudasir A. Mir ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Pcr Amplification ◽  
Its Region ◽  
Fungal Species ◽  
Pathogenicity Test ◽  
Kashmir Valley ◽  
Fusarium Equiseti ◽  
Infected Root ◽  
Fusarium Sp ◽  
High Degree

AbstractChilli (Capsicum annuum L.) is one of the most significant vegetable and spice crop. Wilt caused by Fusarium Sp. has emerged as a serious problem in chilli production. Internal transcribed spacer (ITS) region is widely used as a DNA barcoding marker to characterize the diversity and composition of Fusarium communities. ITS regions are heavily used in both molecular methods and ecological studies of fungi, because of its high degree of interspecific variability, conserved primer sites and multiple copy nature in the genome. In the present study we focused on morphological and molecular characterization of pathogen causing chilli wilt. Chilli plants were collected from four districts of Kashmir valley of Himalayan region. Pathogens were isolated from infected root and stem of the plants. Isolated pathogens were subjected to DNA extraction and PCR amplification. The amplified product was sequenced and three different wilt causing fungal isolates were obtained which are reported in the current investigation. In addition to Fusarium oxysporum and Fusarium solani, a new fungal species was found in association with the chilli wilt in Kashmir valley viz., Fusarium equiseti that has never been reported before from this region. The studies were confirmed by pathogenicity test and re-confirmation by DNA barcoding.

scholarly journals Infrastructural nature

2021 ◽  
pp. 030913252199391
Author(s):  
Sara H Nelson ◽  
Patrick Bigger
Keyword(s):  
Political Economy ◽  
Ecosystem Services ◽  
Strategic Management ◽  
Ecosystem Management ◽  
Human Life ◽  
Ecosystem Functions ◽  
Future Research ◽  
The Political ◽  
Conservation Science ◽  
Conservation Investment

The assertion that ‘ecosystems are infrastructure’ is now common in conservation science and ecosystem management. This article interrogates this infrastructural ontology, which we argue underpins diverse practices of conservation investment and ecosystem management focused on the strategic management of ecosystem functions to sustain and secure human life. We trace the genealogies and geographies of infrastructural nature as an ontology and paradigm of investment that coexists (sometimes in tension) with extractivist commodity regimes. We draw links between literatures on the political economy of ecosystem services and infrastructure and highlight three themes that hold promise for future research: labor, territory, and finance.

scholarly journals A Forensic Detection Method for Hallucinogenic Mushrooms via High-Resolution Melting (HRM) Analysis

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 199
Author(s):  
Xiaochun Zhang ◽  
Huan Yu ◽  
Qi Yang ◽  
Ziwei Wang ◽  
Ruocheng Xia ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Barcoding ◽  
High Resolution Melting ◽  
Its Region ◽  
Its Sequencing ◽  
Melting Temperatures ◽  
Hrm Analysis ◽  
National Drug ◽  
Species Specific ◽  
Its1 And Its2

In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.

scholarly journals Toward a global reference database of COI barcodes for marine zooplankton

2021 ◽  
Vol 168 (6) ◽  
Author(s):  
Ann Bucklin ◽  
Katja T. C. A. Peijnenburg ◽  
Ksenia N. Kosobokova ◽  
Todd D. O’Brien ◽  
Leocadio Blanco-Bercial ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Sequences ◽  
Reference Sequence ◽  
Global Ocean ◽  
Reference Database ◽  
Data Repositories ◽  
Marine Zooplankton ◽  
The North ◽  
Coi Sequences ◽  
Taxonomic Groups

AbstractCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Álvaro J. Benítez ◽  
Dina Ricardo-Caldera ◽  
María Atencia-Pineda ◽  
Jesús Ballesteros-Correa ◽  
Julio Chacón-Pacheco ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Genetic Distances ◽  
Northern Region ◽  
Coi Gene ◽  
Individual Species ◽  
Species Variation ◽  
Molossus Molossus ◽  
Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

Sign in / Sign up

Export Citation Format

Share Document