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      Fungal pathogens occurring on Orthopterida in Thailand

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          Abstract

          Two new fungal genera and six species occurring on insects in the orders Orthoptera and Phasmatodea (superorder Orthopterida) were discovered that are distributed across three families in the Hypocreales. Sixty-seven sequences generated in this study were used in a multi-locus phylogenetic study comprising SSU, LSU, TEF, RPB1 and RPB2 together with the nuclear intergenic region (IGR). These new taxa are introduced as Metarhizium gryllidicola, M. phasmatodeae, Neotorrubiella chinghridicola, Ophiocordyceps kobayasii, O. krachonicola and Petchia siamensis. Petchia siamensis shows resemblance to Cordyceps mantidicola by infecting egg cases (ootheca) of praying mantis (Mantidae) and having obovoid perithecial heads but differs in the size of its perithecia and ascospore shape. Two new species in the Metarhizium cluster belonging to the M. anisopliae complex are described that differ from known species with respect to phialide size, conidia and host. Neotorrubiella chinghridicola resembles Torrubiella in the absence of a stipe and can be distinguished by the production of whole ascospores, which are not commonly found in Torrubiella (except in Torrubiella hemipterigena, which produces multiseptate, whole ascospores) . Ophiocordyceps krachonicola is pathogenic to mole crickets and shows resemblance to O. nigrella, O. ravenelii and O. barnesii in having darkly pigmented stromata. Ophiocordyceps kobayasii occurs on small crickets, and is the phylogenetic sister species of taxa in the ‘sphecocephala’ clade.

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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                Author and article information

                Journal
                Persoonia
                Persoonia
                Persoonia
                Persoonia : Molecular Phylogeny and Evolution of Fungi
                Nationaal Herbarium Nederland & Centraallbureau voor Schimmelcultures
                0031-5850
                1878-9080
                19 February 2020
                June 2020
                : 44
                : 140-160
                Affiliations
                [1 ]Plant Microbe Interaction Research Team, Bioscience and Biotechnology for Agriculture (BBR) BIOTEC, NSTDA, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand;
                [2 ]Center of Excellence in Fungal Research, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand.
                Author notes
                corresponding author e-mail: jajen@ 123456biotec.or.th .
                Article
                10.3767/persoonia.2020.44.06
                7567961
                33116339
                2708da99-7bb3-45d1-8fd5-631833ec1126
                © 2020 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute

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                For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode.Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights.

                History
                : 27 May 2019
                : 7 December 2019
                Categories
                Research Article

                Plant science & Botany
                clavicipitaceae,cordycipitaceae,entomopathogenic fungi,new taxa,ophiocordycipitaceae,taxonomy

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