1
|
Huang YC, Tsai CY, Wang CL. Host Invasion Type Is a Phylogenetically Conserved Characteristic of Cephaleuros. Plant Dis 2023; 107:3222-3229. [PMID: 37005507 DOI: 10.1094/pdis-10-22-2338-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cephaleuros species cause algal spot diseases, also known as red rust diseases, on many plants, including fruit crops. Most algal species are defined based on their morphological characteristics. Recent phylogenetic studies of Cephaleuros species showed that morphological determination was not congruent with phylogeny. Our study examined the phylogenetic congruence of the host invasion types (or growth habits), which are the most critical characteristics in the taxonomy of Cephaleuros. To ensure that host invasion types and phylogenetic characteristics could be inferred from the same isolate, host invasion types were assessed using microanatomical observation, and rRNA sequences from the same algal spot and/or the derived algal cultures were compared. Host invasion types were found to be conserved classification traits and were congruent with Cephaleuros phylogeny. The results also indicated that more than one Cephaleuros species commonly grew on the same leaf or, in a few cases, the same algal spot, suggesting that identification using different algal spots could result in misidentification. The Cephaleuros isolates were separated into two species complexes by host invasion types: the C. virescens species complex (CVSC) with subcuticular host invasion type and the C. parasiticus species complex (CPSC) with intercellular host invasion type. Molecular phylogenetic analysis indicated that Cephaleuros isolates clustered into 14 clades of CVSC and three clades of CPSC. This study also identified 16 and eight new hosts of CVSC and CPSC in Taiwan, respectively.
Collapse
Affiliation(s)
- Yu-Cheng Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Cheng-Yu Tsai
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Chih-Li Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
- Master Program for Plant Medicine and Good Agricultural Practice, National Chung Hsing University, Taichung 402, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402, Taiwan
- Smart Sustainable New Agriculture Research Center (SMARTer), Taichung 402, Taiwan
| |
Collapse
|
2
|
Delavaux CS, Sturmer SL, Wagner MR, Schütte U, Morton JB, Bever JD. Utility of large subunit for environmental sequencing of arbuscular mycorrhizal fungi: a new reference database and pipeline. New Phytol 2021; 229:3048-3052. [PMID: 33190292 DOI: 10.1111/nph.17080] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Camille S Delavaux
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - Sidney L Sturmer
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, R. Antônio da Veiga 140, Blumenau, Santa Catarina, 89030-903, Brazil
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - Ursel Schütte
- Institute of Arctic Biology, University of Alaska Fairbanks, 2140 Koyukuk Drive, Fairbanks, AK, 99775, USA
| | - Joseph B Morton
- West Virginia University, 6 Alegre Pass, Santa Fe, Morgantown, NM, 87508, USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| |
Collapse
|
3
|
Kater L, Mitterer V, Thoms M, Cheng J, Berninghausen O, Beckmann R, Hurt E. Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis. Mol Cell 2020; 79:615-628.e5. [PMID: 32668200 DOI: 10.1016/j.molcel.2020.06.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/13/2020] [Accepted: 06/18/2020] [Indexed: 12/15/2022]
Abstract
Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix12-Ipi32 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
Collapse
Affiliation(s)
- Lukas Kater
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Valentin Mitterer
- Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany
| | - Matthias Thoms
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany; Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany
| | - Jingdong Cheng
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany.
| |
Collapse
|
4
|
Ordynets A, Scherf D, Pansegrau F, Denecke J, Lysenko L, Larsson KH, Langer E. Short-spored Subulicystidium (Trechisporales, Basidiomycota): high morphological diversity and only partly clear species boundaries. MycoKeys 2018; 35:41-99. [PMID: 29997447 PMCID: PMC6031700 DOI: 10.3897/mycokeys.35.25678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/31/2018] [Indexed: 01/16/2023] Open
Abstract
Diversity of corticioid fungi (resupinate Basidiomycota), especially outside the northern temperate climatic zone, remains poorly explored. Furthermore, most of the known species are delimited by morphological concepts only and, not rarely, these concepts are too broad and need to be tested by molecular tools. For many decades, the delimitation of species in the genus Subulicystidium (Hydnodontaceae, Trechisporales) was a challenge for mycologists. The presence of numerous transitional forms as to basidiospore size and shape hindered species delimitation and almost no data on molecular diversity have been available. In this study, an extensive set of 144 Subulicystidium specimens from Paleo- and Neotropics was examined. Forty-nine sequences of ITS nuclear ribosomal DNA region and 51 sequences of 28S nuclear ribosomal DNA region from fruit bodies of Subulicystidium were obtained and analysed within the barcoding gap framework and with phylogenetic Bayesian and Maximum likelihood approaches. Eleven new species of Subulicystidium are described based on morphology and molecular analyses: Subulicystidium boidinii, S. fusisporum, S. grandisporum, S. harpagum, S. inornatum, S. oberwinkleri, S. parvisporum, S. rarocrystallinum, S. robustius, S. ryvardenii and S. tedersooi. Morphological and DNA-evidenced borders were revised for the five previously known species: S. naviculatum, S. nikau, S. obtusisporum, S. brachysporum and S. meridense. Species-level variation in basidiospore size and shape was estimated based on systematic measurements of 2840 spores from 67 sequenced specimens. An updated identification key to all known species of Subulicystidium is provided.
Collapse
Affiliation(s)
- Alexander Ordynets
- Department of Ecology, FB 10 Mathematics and Natural Sciences, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - David Scherf
- Department of Ecology, FB 10 Mathematics and Natural Sciences, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Felix Pansegrau
- Department of Ecology, FB 10 Mathematics and Natural Sciences, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Jonathan Denecke
- Department of Ecology, FB 10 Mathematics and Natural Sciences, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Ludmila Lysenko
- Department of Ecology, FB 10 Mathematics and Natural Sciences, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Karl-Henrik Larsson
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway
| | - Ewald Langer
- Department of Ecology, FB 10 Mathematics and Natural Sciences, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| |
Collapse
|
5
|
Brown SP, Ferrer A, Dalling JW, Heath KD. Don't put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array. Mol Ecol Resour 2016; 16:946-56. [PMID: 26849494 DOI: 10.1111/1755-0998.12507] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/19/2016] [Accepted: 01/23/2016] [Indexed: 01/24/2023]
Abstract
With the increasing democratization of high-throughput sequencing (HTS) technologies, along with the concomitant increase in sequence yield per dollar, many researchers are exploring HTS for microbial community ecology. Many elements of experimental design can drastically affect the final observed community structure, notably the choice of primers for amplification prior to sequencing. Some targeted microbes can fail to amplify due to primer-targeted sequence divergence and be omitted from obtained sequences, leading to differences among primer pairs in the sequenced organisms even when targeting the same community. This potential source of taxonomic bias in HTS makes it prudent to investigate how primer choice will affect the sequenced community prior to investing in a costly community-wide sequencing effort. Here, we use Fluidigm's microfluidic Access Arrays (IFC) followed by Illumina(®) MiSeq Nano sequencing on a culture-derived local mock community to demonstrate how this approach allows for a low-cost combinatorial investigation of primer pairs and experimental samples (up to 48 primer pairs and 48 samples) to determine the most effective primers that maximize obtained communities whilst minimizing taxonomic biases.
Collapse
Affiliation(s)
- Shawn P Brown
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S Goodwin Ave., Urbana, IL, 61801, USA
| | - Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S Goodwin Ave., Urbana, IL, 61801, USA
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S Goodwin Ave., Urbana, IL, 61801, USA.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S Goodwin Ave., Urbana, IL, 61801, USA
| |
Collapse
|
6
|
Gonzaga LL, Costa LEO, Santos TT, Araújo EF, Queiroz MV. Endophytic fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris and have high genetic diversity. J Appl Microbiol 2014; 118:485-96. [PMID: 25410007 DOI: 10.1111/jam.12696] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/04/2014] [Accepted: 11/10/2014] [Indexed: 01/18/2023]
Abstract
AIMS To evaluate the diversity of endophytic fungi from the leaves of the common bean and the genetic diversity of endophytic fungi from the genus Colletotrichum using IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism) analyses. METHODS AND RESULTS The fungi were isolated by tissue fragmentation and identified by analysing the morphological features and sequencing the internal transcribed spacer (ITS) regions and the rDNA large subunit (LSU). Twenty-seven different taxa were identified. Colletotrichum was the most commonly isolated genera from the common bean (32.69% and 24.29% of the total isolates from the Ouro Negro and Talismã varieties, respectively). The IRAP and REMAP analyses revealed a high genetic diversity in the Colletotrichum endophytic isolates and were able to discriminate these isolates from the phytopathogen Colletotrichum lindemuthianum. CONCLUSIONS Fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris endophytic community, and the IRAP and REMAP markers can be used to rapidly distinguish between C. lindemuthianum and other Colletotrichum members that are frequently found as endophytes. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report of the diversity of endophytic fungi present in the common bean and the use of IRAP and REMAP markers to assess the genetic diversity of endophytic fungi from the genus Colletotrichum.
Collapse
Affiliation(s)
- L L Gonzaga
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | | | | |
Collapse
|
7
|
Abstract
Gyromitra is a widespread genus of macroscopic apothecial ascomycetes whose taxa may be mycorrhizal, saprophytic or parasitic. Nuclear ribosomal 28S large subunit sequence data from 35 specimens from North America, along with sequences available in GenBank, were used in maximum-parsimony, maximum-likelihood and Bayesian analyses to reconstruct a phylogeny of Gyromitra in North America. Gyromitra sensu lato forms a monophyletic group within the Discinaceae composed of five distinct subgenera and 11 well supported clades that include Discina, Hydnotrya and Pseudorhizina. A new subgenus is proposed to accommodate G. californica and G. sphaerospora.
Collapse
Affiliation(s)
- Andrew S Methven
- Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois 61920
| | | | | |
Collapse
|
8
|
Henrichs DW, Scott PS, Steidinger KA, Errera RM, Abraham A, Campbell L. Morphology and Phylogeny of Prorocentrum texanum sp. nov. (Dinophyceae): A New Toxic Dinoflagellate from the Gulf of Mexico Coastal Waters Exhibiting Two Distinct Morphologies. J Phycol 2013; 49:143-155. [PMID: 27008396 DOI: 10.1111/jpy.12030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 09/06/2012] [Indexed: 06/05/2023]
Abstract
A new planktonic species of Prorocentrum is described from the Gulf of Mexico. First observed with the Imaging FlowCytobot, Prorocentrum texanum sp. nov. was characterized using LM, SEM, and TEM along with sequencing of the SSU, LSU, and ITS ribosomal regions and the mitochondrial cob and cox1 regions. P. texanum sp. nov. is a round to oval bivalvate dinoflagellate, with a prominent anterior, serrated solid flange on periflagellar a platelet and an opposing short, flat flange on the h platelet. The periflagellar area consists of 10 platelets. Both left and right valves have shallow round depressions and two-sized valve pores. The anterior ejectosome pore pattern differs between the left and right valve in relation to the periflagellar area and margins. Ten to eleven rows of tangential ejectosome pores are present on each valve. P. texanum sp. nov. has two varieties which exhibit distinct morphotypes, one round to oval (var. texanum) and the other pointed (var. cuspidatum). P. texanum var. cuspidatum is morphologically similar to P. micans in surface markings, but is smaller, and has a serrated periflagellar flange, and is genetically distinct from P. micans. Cytologically, P. texanum has two parietal chlo-roplasts, each with a compound, interlamellar pyrenoid, trichocysts, fibrous vesicles that resemble mucocysts, pusules, V- to U-shaped posterior nucleus, golgi, and tubular mitochondria. No genetic difference was found between the two varieties in the five genes examined. Phylogenetic analysis of the SSU, LSU, and ITS ribosomal regions place P. texanum sp. nov. as a sister group to P. micans. One isolate of P. texanum var. texanum produces okadaic acid.
Collapse
Affiliation(s)
- Darren W Henrichs
- Department of Biology, Texas A&M University, College Station, Texas, 77843, USA
| | - Paula S Scott
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, Florida, 33701, USA
| | - Karen A Steidinger
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, Florida, 33701, USA
| | - Reagan M Errera
- Department of Oceanography, Texas A&M University, College Station, Texas, 77843, USA
| | - Ann Abraham
- Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, FDA, Dauphin Island, Alabama, 36528, USA
| | - Lisa Campbell
- Department of Biology, Texas A&M University, College Station, Texas, 77843, USA
- Department of Oceanography, Texas A&M University, College Station, Texas, 77843, USA
| |
Collapse
|
9
|
Athavale SS, Gossett JJ, Hsiao C, Bowman JC, O'Neill E, Hershkovitz E, Preeprem T, Hud NV, Wartell RM, Harvey SC, Williams LD. Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state. RNA 2012; 18:752-8. [PMID: 22334759 PMCID: PMC3312562 DOI: 10.1261/rna.030692.111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.
Collapse
Affiliation(s)
| | | | - Chiaolong Hsiao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Eric O'Neill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Eli Hershkovitz
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | - Stephen C. Harvey
- School of Biology and
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- Corresponding author.E-mail .
| |
Collapse
|