Showing papers by "Conrad L. Schoch published in 2014"
National Institutes of Health1, Centraalbureau voor Schimmelcultures2, University of Perugia3, University of Sydney4, University of Gothenburg5, University of Tennessee6, University of Illinois at Urbana–Champaign7, Royal Botanic Gardens8, University of Tartu9, Purdue University10, Mae Fah Luang University11, Kunming Institute of Botany12, Complutense University of Madrid13, American Museum of Natural History14, University of Pretoria15, Spanish National Research Council16, University of British Columbia17, Academy of Sciences of the Czech Republic18, University of Toronto19, Aberystwyth University20, University of Graz21, University of the Free State22, Commonwealth Scientific and Industrial Research Organisation23, Swedish Museum of Natural History24, Rural Development Administration25, University of California, Davis26, Landcare Research27, Hungarian Academy of Sciences28, Eötvös Loránd University29, Field Museum of Natural History30, University of Szeged31, United States Department of Agriculture32, University of Alabama33, University of Helsinki34, Thailand National Science and Technology Development Agency35, University of Wisconsin-Madison36, National Research Council37, University of North Carolina at Greensboro38, Sungkyunkwan University39, Hirosaki University40, Brandon University41, University of Jena42, University of Findlay43, University of Tübingen44, McMaster University45, Rutgers University46
TL;DR: A set of standards and protocols are proposed to improve the data quality of new sequences, and it is suggested how type and other reference sequences can be used to improve identification of Fungi.
Abstract: DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
360 citations
Duke University1, Kaiserslautern University of Technology2, University of Helsinki3, Yale University4, University of Gdańsk5, University of British Columbia6, Complutense University of Madrid7, Lund University8, National University of Comahue9, University of Barcelona10, University of Oslo11, New York Botanical Garden12, Harvard University13, National Institutes of Health14, University of Liège15, Oregon State University16, University of Arizona17
TL;DR: A multigene phylogenetic synthesis of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences revealing relatively stable relationships for many families and orders is provided.
237 citations
TL;DR: Invasion of L. maculans ‘brassicae’ genome by TEs followed by bursts of TE activity allowed this species to evolve and to better adapt to its host, making this genome species a peculiarity within its own species complex as well as in the Pleosporales lineage.
Abstract: Many plant-pathogenic fungi have a tendency towards genome size expansion, mostly driven by increasing content of transposable elements (TEs). Through comparative and evolutionary genomics, five members of the Leptosphaeria maculans-Leptosphaeria biglobosa species complex (class Dothideomycetes, order Pleosporales), having different host ranges and pathogenic abilities towards cruciferous plants, were studied to infer the role of TEs on genome shaping, speciation, and on the rise of better adapted pathogens. L. maculans ‘brassicae’, the most damaging species on oilseed rape, is the only member of the species complex to have a TE-invaded genome (32.5%) compared to the other members genomes (<4%). These TEs had an impact at the structural level by creating large TE-rich regions and are suspected to have been instrumental in chromosomal rearrangements possibly leading to speciation. TEs, associated with species-specific genes involved in disease process, also possibly had an incidence on evolution of pathogenicity by promoting translocations of effector genes to highly dynamic regions and thus tuning the regulation of effector gene expression in planta. Invasion of L. maculans ‘brassicae’ genome by TEs followed by bursts of TE activity allowed this species to evolve and to better adapt to its host, making this genome species a peculiarity within its own species complex as well as in the Pleosporales lineage.
154 citations
19 Jun 2014
TL;DR: This initial paper focuses on eight genera of appendaged coelomycetes, the type species of which are neo- or epitypified here, and aims to initially focus on the subset of names that have been placed on the “Without-prejudice List of Protected Generic Names of Fungi”.
Abstract: To ensure a stable platform for fungal taxonomy, it is of paramount importance that the genetic application of generic names be based on their DNA sequence data, and wherever possible, not morphology or ecology alone. To facilitate this process, a new database, accessible at www.GeneraofFungi.org (GoF) was established, which will allow deposition of metadata linked to holo-, lecto-, neo- or epitype specimens, cultures and DNA sequence data of the type species of genera. Although there are presently more than 18 000 fungal genera described, we aim to initially focus on the subset of names that have been placed on the "Without-prejudice List of Protected Generic Names of Fungi" (see IMA Fungus 4(2): 381-443, 2013). To enable the global mycological community to keep track of typification events and avoid duplication, special MycoBank Typification identfiers (MBT) will be issued upon deposit of metadata in MycoBank. MycoBank is linked to GoF, thus deposited metadata of generic type species will be displayed in GoF (and vice versa), but will also be linked to Index Fungorum (IF) and the curated RefSeq Targeted Loci (RTL) database in GenBank at the National Center for Biotechnology Information (NCBI). This initial paper focuses on eight genera of appendaged coelomycetes, the type species of which are neo- or epitypified here: Bartalinia (Bartalinia robillardoides; Amphisphaeriaceae, Xylariales), Chaetospermum (Chaetospermum chaetosporum, incertae sedis, Sebacinales), Coniella (Coniella fragariae, Schizoparmaceae, Diaporthales), Crinitospora (Crinitospora pulchra, Melanconidaceae, Diaporthales), Eleutheromyces (Eleutheromyces subulatus, Helotiales), Kellermania (Kellermania yuccigena, Planistromataceae, Botryosphaeriales), Mastigosporium (Mastigosporium album, Helotiales), and Mycotribulus (Mycotribulus mirabilis, Agaricales). Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed below for the major groups of fungi on the List of Protected Generic Names for Fungi.
65 citations