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      Phylogeny of new marine Dothideomycetes and Sordariomycetes from mangroves and deep-sea sediments

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          Abstract

          This paper documents six new saprobic marine fungi and one new genus based on morphology and multi-gene phylogenies. Three Dothideomycetes, and members of the Pleosporales, are introduced: Pseudomassariosphaeria triseptata sp. nov. was recognized as a mangrove species in Amniculicolaceae, and Salsuginea phoenicis sp. nov. was discovered as a second member of Salsugineaceae. A new genus Raghukumaria with Raghukumaria keshaphalae sp. nov., recovered from mangroves, is phylogenetically sister to Halomassarina and nests in the Trematosphaeriaceae. Three new species are referred to the Sordariomycetes: Coniochaeta marina (Coniochaetales, Coniochaetaceae) on driftwood; Fusicolla bharatavarshae (Hypocreales, Nectriaceae) is introduced with asexual and sexual morphs, on decayed mangrove wood of Avicennia marina; and Fusarium sedimenticola (Hypocreales, Nectriaceae) is new to the Fusarium solani species complex (FSSC) from deep-sea sediment.

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          Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species.

          Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.
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            Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit.

            In an effort to establish a suitable alternative to the widely used 18S rRNA system for molecular systematics of fungi, we examined the nuclear gene RPB2, encoding the second largest subunit of RNA polymerase II. Because RPB2 is a single-copy gene of large size with a modest rate of evolutionary change, it provides good phylogenetic resolution of Ascomycota. While the RPB2 and 18S rDNA phylogenies were highly congruent, the RPB2 phylogeny did result in much higher bootstrap support for all the deeper branches within the orders and for several branches between orders of the Ascomycota. There are several strongly supported phylogenetic conclusions. The Ascomycota is composed of three major lineages: Archiascomycetes, Saccharomycetales, and Euascomycetes. Within the Euascomycetes, plectomycetes, and pyrenomycetes are monophyletic groups, and the Pleosporales and Dothideales are distinct sister groups within the Loculoascomycetes. We confirm the placement of Neolecta within the Archiascomycetes, suggesting that fruiting body formation and forcible discharge of ascospores were characters gained early in the evolution of the Ascomycota. These findings show that a slowly evolving protein-coding gene such as RPB2 is useful for diagnosing phylogenetic relationships among fungi.
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              A Beauveria phylogeny inferred from nuclear ITS and EF1-  sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs

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                Author and article information

                Journal
                Botanica Marina
                Walter de Gruyter GmbH
                1437-4323
                0006-8055
                March 26 2020
                March 26 2020
                : 63
                : 2
                : 155-181
                Affiliations
                [1 ]Department of Botany and Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
                [2 ]Fungal Biotechnology Lab, Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
                [3 ]Department of Botany and Microbiology, Faculty of Science, Sohag University, Sohag 82524, Egypt
                [4 ]Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
                [5 ]School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
                [6 ]World Agro Forestry Centre East and Central Asia Office, 132 Lanhei Road, Kunming 650201, P.R. China
                [7 ]Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, P.R. China
                [8 ]Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
                [9 ]Centre of Excellence in Fungal Research, Institute of Excellence in Fungal Research and School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
                [10 ]Emeritus Professor in Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, P.R. China
                [11 ]School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China
                [12 ]Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
                [13 ]State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China
                Article
                10.1515/bot-2019-0014
                58d8f01a-5dea-41ff-b27c-a547e2456ab7
                © 2020
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