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      A new genus and four new species in the /Psathyrella s.l. clade from China

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      Author(s): 1 , , 2 ,
      Publication date (Electronic):
      Journal: MycoKeys
      Publisher: Pensoft Publishers
      Keywords: Agaricales , Basidiomycete, four new taxa, Psathyrellaceae , taxonomy

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          Abstract

          Based on traditional morphological and phylogenetic analyses (ITS, LSU, tef-1α and β-tub) of psathyrelloid specimens collected from China, four new species are here described: Heteropsathyrella macrocystidia , Psathyrella amygdalinospora , P. piluliformoides , and P. truncatisporoides . H. macrocystidia forms a distinct lineage and groups together with Cystoagaricus , Kauffmania , and Typhrasa in the / Psathyrella s.l. clade, based on the Maximum Likelihood and Bayesian analyses. Thus, the monospecific genus Heteropsathyrella gen. nov. is introduced for the single species. Detailed descriptions, colour photos, and illustrations are presented in this paper.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          Kazutaka Katoh, Daron Standley (2013)
          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)
            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

              T.J White, T. Bruns, S. Lee … (1990)
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                Author and article information

                Contributors
                Tolgor Bau
                Jun-Qing Yan:
                ORCID: https://orcid.org/0000-0003-1128-5171
                Journal
                Journal ID (nlm-ta): MycoKeys
                Journal ID (iso-abbrev): MycoKeys
                Journal ID (publisher-id): 11
                Journal ID (index): urn:lsid:arphahub.com:pub:C004A564-9D6A-5F9F-B058-6A3815DFE9C3
                Title: MycoKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1314-4057
                ISSN (Electronic): 1314-4049
                Publication date Collection: 2021
                Publication date (Electronic): 26 May 2021
                Volume: 80
                Pages: 115-131
                Affiliations
                [1 ] Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun 130118, China Jilin Agricultural University Changchun China
                [2 ] Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China Jiangxi Agricultural University Nanchang China
                Author notes
                Corresponding authors: Tolgor Bau ( junwusuo@ 123456126.com ); Jun-Qing Yan ( yanjunqing1990@ 123456126.com )

                Academic editor: Alfredo Vizzini

                Author information
                https://orcid.org/0000-0003-1128-5171
                Article
                Publisher ID: 65123
                DOI: 10.3897/mycokeys.80.65123
                PMC ID: 8172522
                SO-VID: fd882eeb-8775-4df4-9836-ed81b170c2f9
                Copyright © Tolgor Bau, Jun-Qing Yan
                License:

                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
                Date received : 27 February 2021
                Date accepted : 15 May 2021
                Funding
                National Natural Science Foundation of China (32070010 and 31960008); Jiangxi Provincial Natural Science Foundation (20202BABL213041);
                Categories
                Subject: Research Article
                Subject: Agaricales
                Subject: Agaricomycetes
                Subject: Basidiomycota
                Subject: Taxonomy
                Subject: Asia

                Keywords: agaricales ,basidiomycete,four new taxa, psathyrellaceae ,taxonomy
                Data availability:
                Keywords: agaricales , basidiomycete, four new taxa, psathyrellaceae , taxonomy

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