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      A multi-gene phylogeny of Chlorophyllum ( Agaricaceae, Basidiomycota): new species, new combination and infrageneric classification

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          Abstract

          Abstract

          Taxonomic and phylogenetic studies of Chlorophyllum were carried out on the basis of morphological differences and molecular phylogenetic analyses. Based on the phylogeny inferred from the internal transcribed spacer (ITS), the partial large subunit nuclear ribosomal DNA (nrLSU), the second largest subunit of RNA polymerase II ( rpb2) and translation elongation factor 1-α ( tef1) sequences, six well-supported clades and 17 phylogenetic species are recognised. Within this phylogenetic framework and considering the diagnostic morphological characters, two new species, C. africanum and C. palaeotropicum , are described. In addition, a new infrageneric classification of Chlorophyllum is proposed, in which the genus is divided into six sections. One new combination is also made. This study provides a robust basis for a more detailed investigation of diversity and biogeography of Chlorophyllum .

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          Most cited references33

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          Multiple alignment of DNA sequences with MAFFT.

          Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.
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            Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales).

            P. Matheny (2005)
            Approximately 3000 bp across 84 taxa have been analyzed for variable regions of RPB1, RPB2, and nLSU-rDNA to infer phylogenetic relationships in the large ectomycorrhizal mushroom genus Inocybe (Agaricales; Basidiomycota). This study represents the first effort to combine variable regions of RPB1 and RPB2 with nLSU-rDNA for low-level phylogenetic studies in mushroom-forming fungi. Combination of the three loci increases non-parametric bootstrap support, Bayesian posterior probabilities, and resolution for numerous clades compared to separate gene analyses. These data suggest the evolution of at least five major lineages in Inocybe-the Inocybe clade, the Mallocybe clade, the Auritella clade, the Inosperma clade, and the Pseudosperma clade. Additionally, many clades nested within each major lineage are strongly supported. These results also suggest the family Crepiodataceae sensu stricto is sister to Inocybe. Recognition of Inocybe at the family level, the Inocybaceae, is recommended.
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              A Beauveria phylogeny inferred from nuclear ITS and EF1-α sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs

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                Author and article information

                Journal
                MycoKeys
                MycoKeys
                MycoKeys
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2018
                20 March 2018
                : 32
                : 65-90
                Affiliations
                [1 ] Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
                [2 ] National Collection of Fungi, Biosystematics Division, ARC, Plant Health and Protection, Queenswood 9012, Pretoria, South Africa
                [3 ] 111 Koshland Hall 3102, University of California at Berkeley, Berkeley, California 94720-3102, USA
                [4 ] Ecology Division, Biotechnology and Ecology Institute, Ministry of Science and Technology, P.O.Box: 2279, Vientiane Capital, Lao PDR
                [5 ] C/da Calamia 10 – I-87069 San Demetrio Corone (CS), Italy
                Author notes
                Corresponding author: Zai-Wei Ge ( zwge@ 123456mail.kib.ac.cn )

                Academic editor: S. Redhead

                Article
                10.3897/mycokeys.32.23831
                5904524
                d05938de-ed36-4011-a8fe-3ad1b5a188d1
                Zai-Wei Ge, Adriaana Jacobs, Else C. Vellinga, Phongeun Sysouphanthong, Retha van der Walt, Carmine Lavorato, Yi-Feng An, Zhu L. Yang

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 23 January 2018
                : 5 March 2018
                Funding
                the National Natural Science Foundation of China (No. 31461143031 and 31670024)
                Categories
                Research Article

                agaricales,lepiota,macrolepiota,multigene phylogeny,new taxa,fungi,agaricaceae

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