19 research outputs found
Finding needles in haystacks:Linking scientific names, reference specimens and molecular data for Fungi
Get PDFDNA 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. Reannotated
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.The Intramural Research Programs
of the National Center for Biotechnology Information, National
Library of Medicine and the National Human Genome Research
Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201
Finding needles in haystacks : linking scientific names, reference specimens and molecular data for Fungi
Get PDFDNA 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. Reannotated
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.The Intramural Research Programs
of the National Center for Biotechnology Information, National
Library of Medicine and the National Human Genome Research
Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201
Agaricaceae Fr. (Agaricales, Basidiomycota) from areas of Atlantic Forest in Pernambuco, Brazil
Full text linkMolecular characterization of multiple xylanase producing thermophilic/thermotolerant fungi isolated from composting materials
No full textStellate Chlamydospores and Thromboplerous Hyphae in the Mycelium of the Agaric Lepista flaccida
No full textHow well do ITS rDNA sequences differentiate species of true morels (Morchella)?
No full textArguably more mycophiles hunt true morels (Morchella) during their brief fruiting season each spring in the northern hemisphere than any other wild edible fungus. Concerns about overharvesting by individual collectors and commercial enterprises make it essential that science-based management practices and conservation policies are developed to ensure the sustainability of commercial harvests and to protect and preserve morel species diversity. Therefore, the primary objectives of the present study were to: (i) investigate the utility of the ITS rDNA locus for identifying Morchella species, using phylogenetic species previously inferred from multilocus DNA sequence data as a reference; and (ii) clarify insufficiently identified sequences and determine whether the named sequences in GenBank were identified correctly. To this end, we generated 553 Morchella ITS rDNA sequences and downloaded 312 additional ones generated by other researchers from GenBank using emerencia and analyzed them phylogenetically. Three major findings emerged: (i) ITS rDNA sequences were useful in identifying 48/62 (77.4%) of the known phylospecies; however, they failed to identify 12 of the 22 species within the species-rich Elata Subclade and two closely related species in the Esculenta Clade; (ii) at least 66% of the named Morchella sequences in GenBank are misidentified; and (iii) ITS rDNA sequences of up to six putatively novel Morchella species were represented in GenBank. Recognizing the need for a dedicated Web-accessible reference database to facilitate the rapid identification of known and novel species, we constructed Morchella MLST (http://www.cbs.knaw.nl/morchella/), which can be queried with ITS rDNA sequences and those of the four other genes used in our prior multilocus molecular systematic studies of this charismatic genus
