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      Species Diversity of Cordyceps-Like Fungi in the Tiankeng Karst Region of China

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          ABSTRACT

          Tiankeng acts as a refugium for biodiversity amid a changing global climate, and a previous study has shown that some ancient ( Alsophila spinulosa) and unique plants (cool-adapted plants) are present in Tiankeng. However, there are few reports on Ascomycota from the Tiankeng karst region. In this research, the species diversity of Cordyceps-like fungi in Monkey-Ear Tiankeng was investigated. Seven species in the genera Akanthomyces, Beauveria, Cordyceps, and Samsoniella were identified based on internal transcribed spacer sequences and morphological characteristics. Eight new species in the genera Akanthomyces, Cordyceps, and Samsoniella were established and described according to a multilocus phylogenetic analysis and morphological characteristics. Our results revealed that Cordyceps-like fungi were abundant in Monkey-Ear Tiankeng, providing new insights into the diversity of Ascomycota in this special eco-environment.

          IMPORTANCE Karst Tiankeng has a special eco-environment and acts as a refugium for biodiversity. However, there are few reports on Ascomycota from the Tiankeng karst region. In this research, seven known species and eight new species in the genera Akanthomyces, Beauveria, Cordyceps, and Samsoniella were reported. The results showed that Cordyceps-like fungi are abundant in Monkey-Ear Tiankeng. Interestingly, the month of the sampling was November, which is not an active period of growth and reproduction for Cordyceps-like fungi. These results revealed that unconventional time sampling should not be ignored, especially for a special eco-environment, and provided new insights into the diversity of Ascomycota in this special eco-environment.

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

          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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            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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              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                Microbiol Spectr
                Microbiol Spectr
                spectrum
                Microbiology Spectrum
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2165-0497
                12 September 2022
                Sep-Oct 2022
                12 September 2022
                : 10
                : 5
                : e01975-22
                Affiliations
                [a ] Center for Mycomedicine Research, Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, People’s Republic of China
                [b ] Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, Guizhou, People’s Republic of China
                The Ohio State University
                Author notes

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0001-7240-6841
                https://orcid.org/0000-0002-8646-3975
                Article
                01975-22 spectrum.01975-22
                10.1128/spectrum.01975-22
                9603550
                36094103
                5e327348-af28-42d1-8ef5-f85dfc378285
                Copyright © 2022 Chen et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 27 May 2022
                : 2 August 2022
                Page count
                supplementary-material: 0, Figures: 10, Tables: 1, Equations: 0, References: 75, Pages: 17, Words: 9000
                Funding
                Funded by: National Natural Science Foundation of China (NSFC), FundRef https://doi.org/10.13039/501100001809;
                Award ID: 31860002
                Award Recipient :
                Funded by: High-level Innovative Talents Training Object in Guizhou Province;
                Award ID: Qiankehepingtairencai [2020]6005
                Award Recipient :
                Funded by: Science and Technology Foundation of Guizhou Province, FundRef https://doi.org/10.13039/501100004001;
                Award ID: Qiankehejichu [2020]1Y060
                Award Recipient :
                Funded by: Program of Innovative Scientific and technological Talent Team of Guizhou Province;
                Award ID: 2020-5010
                Award Recipient :
                Funded by: Construction Program of Guizhou Engineering Research Center;
                Award ID: Qian Fa Gai Gao Ji 2020-896
                Award Recipient :
                Funded by: Guizhou Science and Technology Support Project;
                Award ID: Qiankehezhicheng [2019]2776
                Award Recipient :
                Categories
                Research Article
                mycology, Mycology
                Custom metadata
                September/October 2022

                tiankeng,ascomycete,cordyceps-like fungi,phylogenetic analysis,morphological

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