Fitopatologia - Artigos
URI permanente para esta coleçãohttps://locus.ufv.br/handle/123456789/11741
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Item Strengthening the interaction of the virology community with the International Committee on Taxonomy of Viruses (ICTV) by linking virus names and their abbreviations to virus species(Systematic Biology, 2019) Zerbini, Francisco Murilo; Calisher, Charles H.; Briese, Thomas; Brister, J. Rodney; Charrel, Rémi N.; Dürrwald, Ralf; Ebihara, Hideki; Fulhorst, Charles F.; Gāo, George Fú; Groschup, Martin H.; Haddow, Andrew D.; Hyndman, Timothy H.; Junglen, Sandra; Klempa, Boris; Klingström, Jonas; Kropinski, Andrew M.; Krupovic, Mart; et al.The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV’s official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.Item Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)(Archives of Virology, 2018-05-12) Zerbini, Francisco Murilo; King, Andrew M. Q.; Lefkowitz, Elliot J.; Mushegian, Arcady R.; Adams, Michael J.; Dutilh, Bas E.; Gorbalenya, Alexander E.; Harrach, Balázs; Harrison, Robert L.; Junglen, Sandra; Knowles, Nick J.; Kropinski, Andrew M.; Krupovic, Mart; Kuhn, Jens H.; Nibert, Max L.; Sabanadzovic, Sead; Rubino, Luisa; et al.This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances. An updated Master Species List incorporating the approved changes was released in March 2018Item The faces of fungi database: fungal names linked with morphology, phylogeny and human impacts(Fungal Diversity, 2015-11-03) Pereira, Olinto L.; Jayasiri, Subashini C.; Hyde, Kevin D.; Ariyawansa, Hiran A.; Bhat, Jayarama; Buyck, Bart; Cai, Lei; Dai, Yu-Cheng; Abd-Elsalam, Kamel A.; Ertz, Damien; Hidayat, Iman; Jeewon, Rajesh; Jones, E. B. Gareth; Bahkali, Ali H.; Karunarathna, Samantha C.; Liu, Jian-Kui; Luangsa-ard, J. Jennifer; et al.Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.Item Improving ITS sequence data for identification of plant pathogenic fungi(Fungal Diversity, 2014-05-15) Pereira, Olinto Liparini; Pinho, Danilo Batista; Nilsson, R. Henrik; Hyde, Kevin D.; Pawłowska, Julia; Ryberg, Martin; Tedersoo, Leho; Aas, Anders Bjørnsgard; Alias, Siti A.; Alves, Artur; Anderson, Cajsa Lisa; Antonelli, Alexandre; Arnold, A. Elizabeth; Bahnmann, Barbara; Bahram, Mohammad; Bengtsson-Palme, Johan; Berlin, Anna; et al.Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.Item Virus taxonomy in the age of metagenomics(Nature Reviews Microbiology, 2017-03) Simmonds, Peter; Adams, Mike J.; Benko, Mária; Breitbart, Mya; Brister, J. Rodney; Zerbini, F. Murilo; Carstens, Eric B.; Davison, Andrew J.; Delwart, Eric; Gorbalenya, Alexander E.; Harrach, Balázs; Hull, Roger; King, Andrew M.Q.; Koonin, Eugene V.; Krupovic, Mart; Kuhn, Jens H.; Lefkowitz, Elliot J.; et al.The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.