65 research outputs found
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
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
Phylogenetic and morphotaxonomic revision of Ramichloridium and allied genera
The phylogeny of the genera Periconiella, Ramichloridium,
Rhinocladiella and Veronaea was explored by means of partial
sequences of the 28S (LSU) rRNA gene and the ITS region (ITS1, 5.8S rDNA and
ITS2). Based on the LSU sequence data, ramichloridium-like species segregate
into eight distinct clusters. These include the Capnodiales
(Mycosphaerellaceae and Teratosphaeriaceae), the
Chaetothyriales (Herpotrichiellaceae), the Pleosporales, and
five ascomycete clades with uncertain affinities. The type species of
Ramichloridium, R. apiculatum, together with R. musae,
R. biverticillatum, R. cerophilum, R. verrucosum, R. pini, and three new
species isolated from Strelitzia, Musa and forest soil,
respectively, reside in the Capnodiales clade. The human-pathogenic
species R. mackenziei and R. basitonum, together with R.
fasciculatum and R. anceps, cluster with Rhinocladiella
(type species: Rh. atrovirens, Herpotrichiellaceae,
Chaetothyriales), and are allocated to this genus. Veronaea
botryosa, the type species of the genus Veronaea, also resides
in the Chaetothyriales clade, whereas Veronaea simplex
clusters as a sister taxon to the Venturiaceae (Pleosporales), and is
placed in a new genus, Veronaeopsis. Ramichloridium
obovoideum clusters with Carpoligna pleurothecii (anamorph:
Pleurothecium sp., Chaetosphaeriales), and a new combination
is proposed in Pleurothecium. Other ramichloridium-like clades
include R. subulatum and R. epichloës (incertae sedis,
Sordariomycetes), for which a new genus, Radulidium is
erected. Ramichloridium schulzeri and its varieties are placed in a
new genus, Myrmecridium (incertae sedis, Sordariomycetes).
The genus Pseudovirgaria (incertae sedis) is introduced to
accommodate ramichloridium-like isolates occurring on various species of rust
fungi. A veronaea-like isolate from Bertia moriformis with
phylogenetic affinity to the Annulatascaceae (Sordariomycetidae) is
placed in a new genus, Rhodoveronaea. Besides
Ramichloridium, Periconiella is also polyphyletic.
Thysanorea is introduced to accommodate Periconiella papuana
(Herpotrichiellaceae), which is unrelated to the type species, P.
velutina (Mycosphaerellaceae)
Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi
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. 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.B.R. and C.L.S. acknowledge support from the Intramural Research
Program of the National Institutes of Health, National Library of
MedicinePeer Reviewe
Finding needles in haystacks:Linking scientific names, reference specimens and molecular data for Fungi
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. 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
H2S biosynthesis and catabolism: new insights from molecular studies
Hydrogen sulfide (H2S) has profound biological effects within living organisms and is now increasingly being considered alongside other gaseous signalling molecules, such as nitric oxide (NO) and carbon monoxide (CO). Conventional use of pharmacological and molecular approaches has spawned a rapidly growing research field that has identified H2S as playing a functional role in cell-signalling and post-translational modifications. Recently, a number of laboratories have reported the use of siRNA methodologies and genetic mouse models to mimic the loss of function of genes involved in the biosynthesis and degradation of H2S within tissues. Studies utilising these systems are revealing new insights into the biology of H2S within the cardiovascular system, inflammatory disease, and in cell signalling. In light of this work, the current review will describe recent advances in H2S research made possible by the use of molecular approaches and genetic mouse models with perturbed capacities to generate or detoxify physiological levels of H2S gas within tissue
Finding needles in haystacks : linking scientific names, reference specimens and molecular data for Fungi
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. 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
Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum
Chaetomium globosum is a filamentous fungus typically isolated from cellulosic substrates. This species also causes superficial infections of humans and, more rarely, can cause cerebral infections. Here, we report the genome sequence of C. globosum isolate CBS 148.51, which will facilitate the study and comparative analysis of this fungus
A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages
Rock surfaces are unique terrestrial habitats in which rapid changes in the intensity of radiation, temperature, water supply and nutrient availability challenge the survival of microbes. A specialised, but diverse group of free-living, melanised fungi are amongst the persistent settlers of bare rocks. Multigene phylogenetic analyses were used to study relationships of ascomycetes from a variety of substrates, with a dataset including a broad sampling of rock dwellers from different geographical locations. Rock-inhabiting fungi appear particularly diverse in the early diverging lineages of the orders Chaetothyriales and Verrucariales. Although these orders share a most recent common ancestor, their lifestyles are strikingly different. Verrucariales are mostly lichen-forming fungi, while Chaetothyriales, by contrast, are best known as opportunistic pathogens of vertebrates (e.g. Cladophialophora bantiana and Exophiala dermatitidis, both agents of fatal brain infections) and saprophytes. The rock-dwelling habit is shown here to be key to the evolution of these two ecologically disparate orders. The most recent common ancestor of Verrucariales and Chaetothyriales is reconstructed as a non-lichenised rock-inhabitant. Ancestral state reconstructions suggest Verrucariales as one of the independent ascomycetes group where lichenisation has evolved on a hostile rock surface that might have favored this shift to a symbiotic lifestyle. Rock-inhabiting fungi are also ancestral to opportunistic pathogens, as they are found in the early diverging lineages of Chaetothyriales. In Chaetothyriales and Verrucariales, specific morphological and physiological traits (here referred to as extremotolerance) evolved in response to stresses in extreme conditions prevailing on rock surfaces. These factors facilitated colonisation of various substrates including the brains of vertebrates by opportunistic fungal pathogens, as well as helped establishment of a stable lichen symbiosis.
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