18
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Diversity of endophytic fungi in the leaflets and branches of Poincianella pyramidalis, an endemic species of Brazilian tropical dry forest

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          ABSTRACT Plants harbour diverse communities of fungal species in their internal compartments. Endophytic fungi help their hosts to establish, survive, and adapt to different environments. Here, we examined the diversity of endophytic fungi in the leaflets and branches of Poincianella pyramidalis, a plant species endemic to the Brazilian tropical dry forest (Caatinga). A total of 360 fragments of leaflets and branches were analysed and 189 endophytic fungi were isolated and distributed among 21 ascomycetous genera based on their ITS and LSU rDNA sequences. Diaporthe was the most frequently identified genus, followed by Didymella and Rhytidhysteron. The colonisation rate of plant fragments was higher in the branches (74 %) than in leaflets (14 %). The richness of the genera of endophytic fungi was also higher in the branches than in leaflets, whereas no difference was observed in endophyte diversity between the plant parts, based on Shannon-Wiener and Fisher alpha diversity indices. Our results indicate that endemic plant species from Brazilian dry forest, such as P. pyramidalis, are predominantly colonised by ascomycetous fungi, especially members of the class Dothideomycetes.

          Related collections

          Most cited references97

          • Record: found
          • Abstract: found
          • Article: not found

          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.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

            Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              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.
                Bookmark

                Author and article information

                Journal
                abb
                Acta Botanica Brasilica
                Acta Bot. Bras.
                Sociedade Botânica do Brasil (Belo Horizonte, BA, Brazil )
                0102-3306
                1677-941X
                December 2020
                : 34
                : 4
                : 755-764
                Affiliations
                [3] Merced orgnameUniversity of California orgdiv1Sierra Nevada Research Institute United States
                [2] Goiânia Goiás orgnameUniversidade Federal de Goiás orgdiv1Instituto de Patologia Tropical e Saúde Pública orgdiv2Departamento de Biociências e Tecnologia Brazil
                [1] Recife Pernambuco orgnameUniversidade Federal de Pernambuco orgdiv1Departamento de Micologia Professor Chaves Batista Brazil
                Article
                S0102-33062020000400755 S0102-3306(20)03400400755
                10.1590/0102-33062020abb0253
                c2fe271d-dd40-42a5-9c4c-4bd01b37d332

                This work is licensed under a Creative Commons Attribution 4.0 International License.

                History
                : 13 September 2020
                : 30 May 2020
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 98, Pages: 10
                Product

                SciELO Brazil

                Self URI: Full text available only in PDF format (EN)
                Categories
                Articles

                Ascomycetous fungi,taxonomy,Dothideomycetes,Diaporthe,Caatinga

                Comments

                Comment on this article