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      A New Marine Species of Miracula ( Oomycota) Parasitic to Minidiscus sp. in Iceland

      research-article
      a , c , a , b
      Mycobiology
      Taylor & Francis
      Bacillariaphyceae, oomycetes, parasitoid, phylogeny, Thalassiosira, one new species

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          Abstract

          Obligate endoparasitic oomycetes are known to ubiquitously occur in marine and freshwater diatoms, but their diversity is still largely unexplored. Many of these parasitoids are members of the early-diverging oomycete lineages ( Miracula, Diatomophthora), others are within the Leptomitales of the Saprolegniomycetes ( Ectrogella, Lagenisma) and some have been described in the Peronosporomycetes ( Aphanomycopsis, Lagenidium). Even though some species have been recently described and two new genera were introduced ( Miracula and Diatomophthora), the phylogeny and taxonomy of most of these organisms remain unresolved. This is contrasted by the high number of sequences from unclassified species, as recently revealed from environmental sequencing, suggesting the presence of several undiscovered species. In this study, a new species of Miracula is reported from a marine centric diatom ( Minidiscus sp.) isolated from Skagaströnd harbor in Northwest Iceland. The morphology and life cycle traits of this novel oomycete parasite are described herein, and its taxonomic placement within the genus Miracula is confirmed by molecular phylogeny. As it cannot be assigned to any previously described species, it is introduced as Miracula islandica in this study. The genus Miracula thus contains three described holocarpic species ( M. helgolandica, M. islandica, M. moenusica) to which likely additional species will need to be added in the future, considering the presence of several lineages known only from environmental sequencing that clustered within the Miracula clade.

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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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            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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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
                Mycobiology
                Mycobiology
                Mycobiology
                Taylor & Francis
                1229-8093
                2092-9323
                16 August 2021
                2021
                : 49
                : 4
                : 355-362
                Affiliations
                [a ]Senckenberg Biodiversity and Climate Research Center , Frankfurt am Main, Germany
                [b ]Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe-Universität Frankfurt am Main , Frankfurt am Main, Germany
                [c ]BioPol ehf, Marine Biotechnology , Skagaströnd, Iceland
                Author notes
                CONTACT Marco Thines m.thines@ 123456thines-lab.eu

                According to a recent suggestion by Thines et al. [ 1], all scientific names are set in italics, regardless of their taxonomic rank.

                Author information
                https://orcid.org/0000-0001-7740-6875
                Article
                1952813
                10.1080/12298093.2021.1952813
                8409938
                34512079
                7fb86ffe-79ea-4793-ba4d-33befc7345c6
                © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group on behalf of the Korean Society of Mycology.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Page count
                Figures: 2, Tables: 0, Pages: 8, Words: 4386
                Categories
                Research Article
                Research Articles

                Plant science & Botany
                bacillariaphyceae,oomycetes,parasitoid,phylogeny,thalassiosira,one new species
                Plant science & Botany
                bacillariaphyceae, oomycetes, parasitoid, phylogeny, thalassiosira, one new species

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