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      Species diversity and major host/substrate associations of the genus Akanthomyces (Hypocreales, Cordycipitaceae)

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          Abstract

          Akanthomyces , a group of fungi with rich morphological and ecological diversity in Cordycipitaceae ( Ascomycota , Hypocreales ), has a wide distribution amongst diverse habitats. By surveying arthropod-pathogenic fungi in China and Southeast Asia over the last six years, nine Akanthomyces spp. were found and identified. Five of these were shown to represent four known species and an undetermined species of Akanthomyces . Four of these were new species and they were named A. kunmingensis and A. subaraneicola from China, A. laosensis from Laos and A. pseudonoctuidarum from Thailand. The new species were described and illustrated according to the morphological characteristics and molecular data. Akanthomyces araneogenus , which was isolated from spiders from different regions in China, Thailand and Vietnam, was described as a newly-recorded species from Thailand and Vietnam. The phylogenetic positions of the nine species were evaluated, based on phylogenetic inferences according to five loci, namely, ITS, nrLSU, TEF, RPB1 and RPB2. In this study, we reviewed the research progress achieved for Akanthomyces regarding its taxonomy, species diversity, geographic distribution and major host/substrate associations. The morphological characteristics of 35 species in Akanthomyces , including four novel species and 31 known taxa, were also compared.

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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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            MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

            We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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              IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

              Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
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                Author and article information

                Contributors
                Journal
                MycoKeys
                MycoKeys
                11
                urn:lsid:arphahub.com:pub:C004A564-9D6A-5F9F-B058-6A3815DFE9C3
                urn:lsid:zoobank.org:pub:A4FD9303-3F01-45D9-B438-FCCFE465D2F7
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2024
                15 January 2024
                : 101
                : 113-141
                Affiliations
                [1 ] Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, China
                [2 ] The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, Yunnan, China
                [3 ] Faculty of Agricultural Production, Maejo University, Chiang Mai, Thailand
                [4 ] Institute of Regional Research and Development, Ministry of Science and Technology, Hanoi, Vietnam
                Author notes
                Corresponding author: Hong Yu ( hongyu@ 123456ynu.edu.cn ; herbfish@ 123456163.com)

                Academic editor: R. Phookamsak

                Author information
                https://orcid.org/0000-0002-1262-6700
                https://orcid.org/0000-0002-2149-5714
                Article
                109751
                10.3897/mycokeys.101.109751
                10806914
                38269036
                9e8e939c-c13a-4df1-82c9-7c0fdd5d0334
                Yao Wang, Zhi-Qin Wang, Run Luo, Sisommay Souvanhnachit, Chinnapan Thanarut, Van-Minh Dao, Hong Yu

                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
                : 19 July 2023
                : 19 December 2023
                Funding
                This work was supported by the National Natural Science Foundation of China (No. 31870017 and 32200013).
                Categories
                Research Article
                Cordycipitaceae
                Hypocreales
                Sordariomycetes
                Taxonomy
                Asia
                China

                arthropod-pathogenic fungi,cordycipitaceae,morphology,new species,phylogenetic analyses

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