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      New species and records of Diaporthe from Jiangxi Province, China

      1 , 2 , 3 , 1 , , 1

      MycoKeys

      Pensoft Publishers

      DNA phylogeny, five new taxa, forest trees, systematics, taxonomy

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          Abstract

          Diaporthe species have often been reported as important plant pathogens, saprobes and endophytes on a wide range of plant hosts. Although several Diaporthe species have been recorded, little is known about species able to infect forest trees in Jiangxi Province. Hence, extensive surveys were recently conducted in Jiangxi Province, China. A total of 24 isolates were identified and analysed using comparisons of DNA sequence data for the nuclear ribosomal internal transcribed spacer (ITS), calmodulin ( cal), histone H3 ( his3), partial translation elongation factor-1α ( tef1) and β-tubulin ( tub2) gene regions, as well as their morphological features. Results revealed five novel taxa, D. bauhiniae , D. ganzhouensis , D. schimae , D. verniciicola , D. xunwuensis spp. nov. and three known species, D. apiculatum , D. citri and D. multigutullata .

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          Most cited references 57

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          New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

          PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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            MrBayes 3: Bayesian phylogenetic inference under mixed models.

            MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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              jModelTest 2: more models, new heuristics and parallel computing.

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                Author and article information

                Contributors
                Journal
                MycoKeys
                MycoKeys
                11
                urn:lsid:arphahub.com:pub:C004A564-9D6A-5F9F-B058-6A3815DFE9C3
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2021
                14 January 2021
                : 77
                : 41-64
                Affiliations
                [1 ] The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
                [2 ] Forestry Biotechnology Hunan Key Laboratories, Central South University of Forestry and Technology, Changsha 410004, China
                [3 ] The Key Laboratory for Non-Wood Forest Cultivation and Conservation of the Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
                Author notes
                Corresponding author: Cheng-Ming Tian ( chengmt@ 123456bjfu.edu.cn )

                Academic editor: A. Miller

                Article
                59999
                10.3897/mycokeys.77.59999
                7819952
                Qin Yang, Ning Jiang, Cheng-Ming Tian

                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.

                Funding
                the National Natural Science Foundation of China (Project No.: 31670647); the Research Foundation of Education Bureau of Hunan Province, China (Project No.: 19B608) and the introduction of talent research start-up fund project of CSUFT (Project No.: 2019YJ025).
                Categories
                Research Article
                Ascomycota
                Molecular Systematics
                Phylogeny
                Taxonomy
                Asia

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