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      Phylogeny and taxonomy of three new Ctenomyces (Arthrodermataceae, Onygenales) species from China

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      MycoKeys

      Pensoft Publishers

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          Abstract

          Twelve Ctenomyces (Arthrodermataceae, Onygenales) strains were obtained and identified during a survey of keratinophilic fungi in soils from China. We used molecular identification combined with morphological evidence to delimit species, circumscribing five species in the genus. Three new species are herein described: C.albus sp. nov., C.obovatus sp. nov. and C.peltricolor sp. nov. We also described, illustrated and compared the novel species with related species in the morphology.

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

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            Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data

            Motivation: The current molecular data explosion poses new challenges for large-scale phylogenomic analyses that can comprise hundreds or even thousands of genes. A property that characterizes phylogenomic datasets is that they tend to be gappy, i.e. can contain taxa with (many and disparate) missing genes. In current phylogenomic analyses, this type of alignment gappyness that is induced by missing data frequently exceeds 90%. We present and implement a generally applicable mechanism that allows for reducing memory footprints of likelihood-based [maximum likelihood (ML) or Bayesian] phylogenomic analyses proportional to the amount of missing data in the alignment. We also introduce a set of algorithmic rules to efficiently conduct tree searches via subtree pruning and re-grafting moves using this mechanism. Results: On a large phylogenomic DNA dataset with 2177 taxa, 68 genes and a gappyness of 90%, we achieve a memory footprint reduction from 9 GB down to 1 GB, a speedup for optimizing ML model parameters of 11, and accelerate the Subtree Pruning Regrafting tree search phase by factor 16. Thus, our approach can be deployed to improve efficiency for the two most important resources, CPU time and memory, by up to one order of magnitude. Availability: Current open-source version of RAxML v7.2.6 available at http://wwwkramer.in.tum.de/exelixis/software.html. Contact: stamatak@cs.tum.edu
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              Keratinophilic fungi of poultry farm and feather dumping soil in Tamil Nadu, India.

              Soils of 10 poultry farms from Namakkal and 12 feather dumping sites from Chennai were studied for the presence of keratinophilic fungi. A total of 34 species belonging to 19 genera and one non-sporulating fungus were recovered. Sixteen species of fungi and one non-sporulating fungi were common to both sites, eight species were specific to Namakkal and nine species were specific to Chennai. Dermatophytes and closely related fungi were represented by six species belonging to five genera. Fungal species commonly found in the soil samples included Chrysosporium keratinophilum (73%), Trichophyton mentagrophytes (68.2%), Microsporum gypseum (64%), Myceliopthora vellerea (32%), Chrysosporium state of Arthroderma tuberculatum (27.3%) and Geomyces pannorum (23%). Non-dermatophyte fungi were represented by 28 species belonging to 14 genera and one non-sporulating fungus.
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                Author and article information

                Journal
                MycoKeys
                MC
                Pensoft Publishers
                1314-4049
                1314-4057
                February 20 2019
                February 20 2019
                : 47
                : 1-16
                Article
                10.3897/mycokeys.47.30740
                © 2019

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