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      Two new species of Hymenochaetaceae from tropical Asia and America

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          Abstract

          Two new species in Hymenochaetaceae, Fulvifomes acaciae and Pyrrhoderma nigra, are illustrated and described from tropical Asia and America based on morphology and phylogenetic analyses. F. acaciae is characterized by perennial, pileate, and woody hard basidiomata when fresh; ash gray to dark gray, encrusted, concentrically sulcate, and irregularly cracked pileal surface; circular pores of 7–8 per mm with entire dissepiments; a dimitic hyphal system in trama and context; absence of setal element and presence of cystidioles; and broadly ellipsoid, yellowish brown, thick-walled, and smooth basidiospores measuring 5–6 μm × 4–5 μm. P. nigra is characterized by perennial and resupinate basidiomata with dark gray to almost black pore surface when fresh; small and circular pores of 7–9 per mm, a monomitic hyphal system with generative hyphae simple septate, hyphoid setae dominant in subiculum but not in tube trama, and absence of cystidia; and ellipsoid, hyaline, thin-walled basidiospores measuring 4–5 μm × 3–3.6 μm. The differences between the new species and morphologically similar and phylogenetically related species are discussed. Keys to Fulvifomes and Pyrrhoderma have also been provided.

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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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            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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              AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

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                Author and article information

                Contributors
                Journal
                Front Cell Infect Microbiol
                Front Cell Infect Microbiol
                Front. Cell. Infect. Microbiol.
                Frontiers in Cellular and Infection Microbiology
                Frontiers Media S.A.
                2235-2988
                19 January 2023
                2022
                : 12
                : 1100044
                Affiliations
                [1] 1 Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University , Beijing, China
                [2] 2 College of Pharmacy and Life Sciences, Jiujiang University , Jiujiang, China
                [3] 3 Faculty of Agronomy and Life Sciences, Zhaotong University , Zhaotong, China
                [4] 4 Urb. Bellas Lomas , Mayaguez, Puerto Rico
                [5] 5 Biology Centre of the Academy of Sciences of the Czech Republic , České Budějovice, Czechia
                Author notes

                Edited by: Jia-Jia Chen, Jiangsu Vocational College of Agriculture and Forestry, China

                Reviewed by: Junzhi Qiu, Fujian Agriculture and Forestry University, China; Chang-lin Zhao, Southwest Forestry University, China

                *Correspondence: Yuan Yuan, yuanyuan1018@ 123456bjfu.edu.cn ; Josef Vlasák, vlasak@ 123456umbr.cas.cz

                This article was submitted to Fungal Pathogenesis, a section of the journal Frontiers in Cellular and Infection Microbiology

                Article
                10.3389/fcimb.2022.1100044
                9892452
                fc15a89c-d7a6-4718-b820-cd965b4567d9
                Copyright © 2023 Zhou, Ji, Liu, Miller, Yuan and Vlasák

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 16 November 2022
                : 23 December 2022
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 49, Pages: 14, Words: 5820
                Funding
                Funded by: National Natural Science Foundation of China , doi 10.13039/501100001809;
                Award ID: 32161143013, 32011540380
                Funded by: Akademie Věd České Republiky , doi 10.13039/501100004240;
                Award ID: 60077344
                The research was financed by National Natural Science Foundation of China (Project Nos. 32161143013 and 32011540380) and by the institutional support of the Academy Sciences of the Czech Republic (RVO: 60077344).
                Categories
                Cellular and Infection Microbiology
                Original Research

                Infectious disease & Microbiology
                white rot,hymenochaetaceae,polypore,taxonomy,wood-decaying fungi
                Infectious disease & Microbiology
                white rot, hymenochaetaceae, polypore, taxonomy, wood-decaying fungi

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