New saprobic marine fungi and a new combination
TL;DR: Five new saprobic marine fungi occurring on various substrata in the marine environment are documents, including Bacusphaeria nypae gen. et sp.
Abstract: Abstract This paper documents five new saprobic marine fungi occurring on various substrata in the marine environment. Bacusphaeria nypae gen. et sp. nov. was discovered on bases of fronds of Nypa fruticans in Malaysia and phylogenetically, it belongs to the Tirisporellaceae (Tirisporellales, Diaporthomycetidae, Sordariomycetes) based on 18S and 28S rDNA. Cryptovalsa avicenniae, Ceriosporopsis minuta and Jattaea mucronata also belong to the Sordariomycetes; Cr. avicenniae was saprobic on Avicennia marina collected in Saudi Arabia, J. mucronata on intertidal decaying bark of Rhizophora mucronata while Ce. minuta was found on driftwood collected on a sandy beach in Japan. Phylogeny based on 18S and 28S rDNA placed Cr. avicenniae with other Cryptovalsa species in the Diatrypaceae. Jattaea mucronata groups well in the Calosphaeriales and is closely related to J. algeriensis based on a phylogeny using ITS and 28S rRNA and RPB2 genes. Aegeanispora elanii gen. et sp. nov. is an asexual fungus which produces pycnidia on decaying driftwood collected in the Aegean Sea. Combined 18S and 28S rDNA phylogenetic analyses suggest that it is a member of the Pleosporales, Dothideomycetes. Ceriosporopsis minuta resembles C. capillacea with its tubular, long polar appendages of ascospores but dimensions of ascomata and ascospores for the former species are considerably smaller. Ceriosporopsis is considered the best genus to accommodate C. minuta without support from sequence data. Sammeyersia is established as a new genus to accommodate Lulworthia grandispora, a species unrelated to Lulworthia fucicola, the type species. The diagnostic characteristic for the genus is a melanized region at the base of the neck of the ascomata.
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TL;DR: This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names.
Abstract: Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10–15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of Lalaria, which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).
243 citations
TL;DR: Both asexual and sexual genera are merged into one outline for the phylum Ascomycota, which comprises of three subphyla viz.
Abstract: Taxonomic placement of genera have been changing rapidly as taxonomists widely use DNA sequence data in phylogenetic and evolutionary studies It is essential to update existing databases/outlines based on recent studies, since these sources are widely used as a foundation for other research In this outline, we merge both asexual and sexual genera into one outline The phylum Ascomycota comprises of three subphyla viz Pezizomycotina (including 13 classes, 124 orders and 507 families), Saccharomycotina (including one class, one order and 13 families) and Taphrinomycotina (five classes, five orders and six families) Approximately, 6600 genera have been listed under different taxonomic ranks including auxiliary (intermediate) taxonomic ranks
222 citations
Cites background from "New saprobic marine fungi and a new..."
...Daruvedia Dennis Dokmaia I. Promputtha Farasanispora Abdel-Wahab et al. Foliophoma Crous* Fusculina Crous & Summerell Glaxoa P.F. Cannon Gordonomyces Crous & Marinc....
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...Pleosporales genera incertae sedis Aegeanispora E.B.G. Jones & Abdel-Wahab* Antealophiotrema A. Hashim....
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...Jones & Abdel-Wahab Abdel-Wahab et al. (2017) introduced this coelomycetous genus and showed that it belongs in Pleosporales genera incertae sedis....
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...Ligninsphaeria J.F. Zhang et al. Lindgomycetaceae K. Hiray. et al. Arundellina Wanas. et al. Clohesyomyces K.D. Hyde Hongkongmyces Tsang et al. Lindgomyces K. Hiray. et al. Lolia Abdel-Aziz & Abdel-Wahab Longipedicellataceae Phukhams. et al. Longipedicellata H. Zhang et al. Pseudoxylomyces Kaz....
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...Corollospora Werderm Cucullosporella K.D. Hyde & E.B.G. Jones Ebullia K.L. Pang Fluviatispora K.D. Hyde Gesasha Abdel-Wahab & Nagah....
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TL;DR: This treatment of the class Sordariomycetes provides up-to-date DNA based phylogenies for 45 orders and 163 families and provides general descriptions and illustrate the type genus or another genus, where the placement has generally been confirmed with molecular data.
Abstract: This is a continuation of the papers “Towards a classification of Sordariomycetes” (2015) and “Families of Sordariomycetes” (2016) in which we compile a treatment of the class Sordariomycetes. The present treatment is needed as our knowledge has rapidly increased, from 32 orders, 105 families and 1331 genera in 2016, to 45 orders, 167 families and 1499 genera (with 308 genera incertae sedis) at the time of publication. In this treatment we provide notes on each order, families and short notes on each genus. We provide up-to-date DNA based phylogenies for 45 orders and 163 families. Three new genera and 16 new species are introduced with illustrations and descriptions, while 23 new records and three new species combinations are provided. We also list 308 taxa in Sordariomycetes genera incertae sedis. For each family we provide general descriptions and illustrate the type genus or another genus, the latter where the placement has generally been confirmed with molecular data. Both the sexual and asexual morphs representative of a family are illustrated where available. Notes on ecological and economic considerations are also given.
213 citations
Cites background from "New saprobic marine fungi and a new..."
...Sammeyersia grandispora is identified by the length of the ascospores over 400 μm (Abdel-Wahab et al. 2017)....
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TL;DR: This article reviews knowledge of marine fungi covering a wide range of topics: their higher classification, ecology and world distribution, role in energy transfer in the oceans, origin and new chemical structures.
Abstract: Index Fungorum, Species Fungorum and MycoBank are the key fungal nomenclature and taxonomic databases that can be sourced to find taxonomic details concerning fungi, while DNA sequence data can be sourced from the NCBI, EBI and UNITE databases. Nomenclature and ecological data on freshwater fungi can be accessed on http://fungi.life.illinois.edu/
, while http://www.marinespecies.org/provides
a comprehensive list of names of marine organisms, including information on their synonymy. Previous websites however have little information on marine fungi and their ecology, beside articles that deal with marine fungi, especially those published in the nineteenth and early twentieth centuries may not be accessible to those working in third world countries. To address this problem, a new website www.marinefungi.org
was set up and is introduced in this paper. This website provides a search facility to genera of marine fungi, full species descriptions, key to species and illustrations, an up to date classification of all recorded marine fungi which includes all fungal groups (Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota and fungus-like organisms e.g. Thraustochytriales), and listing recent publications. Currently, 1257 species are listed in the marine fungi website (
www.marinefungi.org
), in 539 genera, 74 orders, 168 families, 20 classes and five phyla, with new taxa continuing to be described. The website has curators with specialist mycological expertise who help to provide update data on the classification of marine fungi. This article also reviews knowledge of marine fungi covering a wide range of topics: their higher classification, ecology and world distribution, role in energy transfer in the oceans, origin and new chemical structures. An updated classification of marine fungi is also included. We would like to invite all mycologists to contribute to this innovative website.
114 citations
TL;DR: This study obtained the type specimens or other authentic specimens of diaporthalean taxa from worldwide fungaria, and based on morphological characters from type or authentic specimens, details from protologue and original illustrations and molecular data obtained from GenBank, accepts 27 families and 138 genera within Diaporthales, and places Tirisporellaceae and one genus in Xylariomycetidae genera incertae sedis.
Abstract: Demarcation of family, genus and species boundaries in the Diaporthales has been tentative due to uninformative illustrations and descriptions, overlapping morphological characteristics, misplacement or poor condition of type specimens and shortage of molecular data from ex-type cultures. In this study, we obtained the type specimens or other authentic specimens of diaporthalean taxa from worldwide fungaria. We examined, described and illustrated them. This study is based on morphological characters from type or authentic specimens, details from protologue and original illustrations and molecular data obtained from GenBank. Combined analyses of nrITS, nrLSU, RPB2 and TEF1-α sequence data were used to construct the molecular phylogeny. Additionally, we provided separate phylogenetic trees for families when necessary to show the generic distribution within these families based on suitable gene markers. Based on morphology and phylogeny, we treat 17 genera previously assigned to Diaporthales genera incertae sedis within several families. For some genera we have designated new generic types as they are lacking type species or type species have affiliations with other families. We exclude Anisomycopsis from Diaporthales and place it in Xylariomycetidae genera incertae sedis. Tirisporellaceae, which was previously placed in Tirisporellales is placed in Diaporthales based on phylogeny and morphology. A new combination, Dendrostoma leiphaemia propose for Amphiporthe leiphaemia (Fr.) Butin. Based on the morphological characters and molecular data we accept 27 families and 138 genera within Diaporthales, 24 genera in Diaporthales genera incertae sedis and one genus in Xylariomycetidae genera incertae sedis. We provide notes for genera in Diaporthales genera incertae sedis, and excluded and doubtful genera are listed with notes on their taxonomy and phylogeny.
58 citations
References
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01 Jan 1990
26,241 citations
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
Abstract: Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
20,627 citations
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Abstract: Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Γ yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets ≥4000 taxa it also runs 2--3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25 057 (1463 bp) and 2182 (51 089 bp) taxa, respectively.
Availability: icwww.epfl.ch/~stamatak
Contact: Alexandros.Stamatakis@epfl.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
14,847 citations
23 Dec 2010
TL;DR: Development of the CIPRES Science Gateway is described, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources.
Abstract: Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
9,117 citations
"New saprobic marine fungi and a new..." refers methods in this paper
...One hundred successive Figure 56: Maximum likelihood (ML) analysis was performed for species in Jattaea, Calosphaeria and Togniniella at the CIPRES webportal (Miller et al. 2010) using RAxML v....
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