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Dreyling L, Boch S, Lumbsch HT, Schmitt I. Surveying lichen diversity in forests: A comparison of expert mapping and eDNA metabarcoding of bark surfaces. MycoKeys 2024; 106:153-172. [PMID: 38948916 PMCID: PMC11214015 DOI: 10.3897/mycokeys.106.117540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 07/02/2024] Open
Abstract
Lichens are an important part of forest ecosystems, contributing to forest biodiversity, the formation of micro-niches and nutrient cycling. Assessing the diversity of lichenised fungi in complex ecosystems, such as forests, requires time and substantial skills in collecting and identifying lichens. The completeness of inventories thus largely depends on the expertise of the collector, time available for the survey and size of the studied area. Molecular methods of surveying biodiversity hold the promise to overcome these challenges. DNA barcoding of individual lichen specimens and bulk collections is already being applied; however, eDNA methods have not yet been evaluated as a tool for lichen surveys. Here, we assess which species of lichenised fungi can be detected in eDNA swabbed from bark surfaces of living trees in central European forests. We compare our findings to an expert floristic survey carried out in the same plots about a decade earlier. In total, we studied 150 plots located in three study regions across Germany. In each plot, we took one composite sample based on six trees, belonging to the species Fagussylvatica, Piceaabies and Pinussylvestris. The eDNA method yielded 123 species, the floristic survey 87. The total number of species found with both methods was 167, of which 48% were detected only in eDNA, 26% only in the floristic survey and 26% in both methods. The eDNA contained a higher diversity of inconspicuous species. Many prevalent taxa reported in the floristic survey could not be found in the eDNA due to gaps in molecular reference databases. We conclude that, currently, eDNA has merit as a complementary tool to monitor lichen biodiversity at large scales, but cannot be used on its own. We advocate for the further development of specialised and more complete databases.
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Affiliation(s)
- Lukas Dreyling
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, GermanySenckenberg Biodiversity and Climate Research Centre (SBiK-F)Frankfurt am MainGermany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main, GermanyGoethe University FrankfurtFrankfurt am MainGermany
| | - Steffen Boch
- WSL Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, SwitzerlandWSL Swiss Federal Institute for Forest, Snow and Landscape ResearchBirmensdorfSwitzerland
| | - H. Thorsten Lumbsch
- Collections, Conservation, and Research, The Field Museum, Chicago, IL 60605-2496, USAThe Field MuseumChicagoUnited States of America
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, GermanySenckenberg Biodiversity and Climate Research Centre (SBiK-F)Frankfurt am MainGermany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main, GermanyGoethe University FrankfurtFrankfurt am MainGermany
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Doering JA, Booth T, Wiersma YF, Piercey-Normore MD. How do genes flow? Identifying potential dispersal mode for the semi-aquatic lichen Dermatocarpon luridum using spatial modelling and photobiont markers. BMC Ecol 2020; 20:56. [PMID: 33059667 PMCID: PMC7565318 DOI: 10.1186/s12898-020-00324-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 10/07/2020] [Indexed: 11/10/2022] Open
Abstract
Background Landscape genetics is an interdisciplinary field that combines tools and techniques from population genetics with the spatially explicit principles from landscape ecology. Spatial variation in genotypes is used to test hypotheses about how landscape pattern affects dispersal in a wide range of taxa. Lichens, symbiotic associations between mycobionts and photobionts, are an entity for which little is known about their dispersal mechanism. Our objective was to infer the dispersal mechanism in the semi-aquatic lichen Dermatocarpon luridum using spatial models and the spatial variation of the photobiont, Diplosphaera chodatii. We sequenced the ITS rDNA and the β-actin gene regions of the photobiont and mapped the haplotype spatial distribution in Payuk Lake. We subdivided Payuk Lake into subpopulations and applied four spatial models based on the topography and hydrology to infer the dispersal mechanism. Results Genetic variation corresponded with the topography of the lake and the net flow of water through the waterbody. A lack of isolation-by-distance suggests high gene flow or dispersal within the lake. We infer the dispersal mechanism in D. luridum could either be by wind and/or water based on the haplotype spatial distribution of its photobiont using the ITS rDNA and β-actin markers. Conclusions We inferred that the dispersal mechanism could be either wind and/or water dispersed due to the conflicting interpretations of our landscape hypotheses. This is the first study to use spatial modelling to infer dispersal in semi-aquatic lichens. The results of this study may help to understand lichen dispersal within aquatic landscapes, which can have implications in the conservation of rare or threatened lichens.
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Affiliation(s)
- Jennifer A Doering
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
| | - Tom Booth
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Yolanda F Wiersma
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada
| | - Michele D Piercey-Normore
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,School of Science and Environment, Grenfell Campus, Memorial University of Newfoundland, Corner Brook, NL, A2H 5G4, Canada
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Wilken PM, Aylward J, Chand R, Grewe F, Lane FA, Sinha S, Ametrano C, Distefano I, Divakar PK, Duong TA, Huhndorf S, Kharwar RN, Lumbsch HT, Navathe S, Pérez CA, Ramírez-Berrutti N, Sharma R, Sun Y, Wingfield BD, Wingfield MJ. IMA Genome - F13: Draft genome sequences of Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti. IMA Fungus 2020; 11:19. [PMID: 33014691 PMCID: PMC7513301 DOI: 10.1186/s43008-020-00039-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Draft genomes of the fungal species Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti are presented. Physcia stellaris is an important lichen forming fungus and Ambrosiella cleistominuta is an ambrosia beetle symbiont. Cercospora brassicicola and C. citrullina are agriculturally relevant plant pathogens that cause leaf-spots in brassicaceous vegetables and cucurbits respectively. Teratosphaeria pseudoeucalypti causes severe leaf blight and defoliation of Eucalyptus trees. These genomes provide a valuable resource for understanding the molecular processes in these economically important fungi.
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Affiliation(s)
- P. Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Felix Grewe
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Frances A. Lane
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
| | - Shagun Sinha
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Claudio Ametrano
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Isabel Distefano
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Pradeep K. Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Tuan A. Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
| | - Sabine Huhndorf
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Ravindra N. Kharwar
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - H. Thorsten Lumbsch
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Sudhir Navathe
- Agharkar Research Institute, G.G. Agharkar Road, Pune, 411004 India
| | - Carlos A. Pérez
- Department of Plant Protection, EEMAC, Facultad de Agronomía, UdelaR, Paysandú, Uruguay
| | | | - Rohit Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, S.P, Pune University, Pune, 411 007 India
| | - Yukun Sun
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
| | - Michael J. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
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Bradshaw M, Grewe F, Thomas A, Harrison CH, Lindgren H, Muggia L, St Clair LL, Lumbsch HT, Leavitt SD. Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi. BMC Evol Biol 2020; 20:2. [PMID: 31906844 PMCID: PMC6945747 DOI: 10.1186/s12862-019-1571-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/19/2019] [Indexed: 02/08/2023] Open
Abstract
Background Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. Results We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of this complex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, intergenic spacer region, and some intronic regions, independently; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. Conclusions The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.
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Affiliation(s)
- Michael Bradshaw
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Felix Grewe
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL, USA
| | - Anne Thomas
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Cody H Harrison
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | | | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127, Trieste, Italy
| | - Larry L St Clair
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA.,M. L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | | | - Steven D Leavitt
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA. .,M. L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA.
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Han J, Zhang L, Wang P, Yang G, Wang S, Li Y, Pan K. Heterogeneity of intron presence/absence in Olifantiella sp. (Bacillariophyta) contributes to the understanding of intron loss. JOURNAL OF PHYCOLOGY 2018; 54:105-113. [PMID: 29120060 DOI: 10.1111/jpy.12605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 11/01/2017] [Indexed: 06/07/2023]
Abstract
Although hypotheses have been proposed and developed to interpret the origins and functions of introns, substantial controversies remain about the mechanism of intron evolution. The availability of introns in the intermediate state is quite helpful for resolving this debate. In this study, a new strain of diatom (denominated as DB21-1) was isolated and identified as Olifantiella sp., which possesses multiple types of 18S rDNAs (obtained from genomic DNA; lengths ranged from 2,056 bp to 2,988 bp). Based on alignments between 18S rDNAs and 18S rRNA (obtained from cDNA; 1,783 bp), seven intron insertion sites (IISs) located in the 18S rDNA were identified, each of which displayed the polymorphism of intron presence/absence. Specific primers around each IIS were designed to amplify the introns and the results indicated that introns in the same IIS varied in lengths, while terminal sequences were conserved. Our study showed that the process of intron loss happens via a series of successive steps, and each step could derive corresponding introns under intermediate states. Moreover, these results indicate that the mechanism of genomic deletion that occurs at DNA level can also lead to exact intron loss.
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Affiliation(s)
- Jichang Han
- Laboratory of Applied Microalgae Biology, Ocean University of China, Qingdao, 266003, China
| | - Lin Zhang
- College of Marine, Ningbo University, Ningbo, 315211, China
| | - Pu Wang
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, 55018, USA
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Song Wang
- Laboratory of Applied Microalgae Biology, Ocean University of China, Qingdao, 266003, China
| | - Yuhang Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Kehou Pan
- Laboratory of Applied Microalgae Biology, Ocean University of China, Qingdao, 266003, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
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Papaioannou IA, Dimopoulou CD, Typas MA. "Cryptic" group-I introns in the nuclear SSU-rRNA gene of Verticillium dahliae. Curr Genet 2013; 60:135-48. [PMID: 24258678 DOI: 10.1007/s00294-013-0417-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/24/2013] [Accepted: 11/06/2013] [Indexed: 11/30/2022]
Abstract
Group-I introns are widespread--though irregularly distributed--in eukaryotic organisms, and they have been extensively used for discrimination and phylogenetic analyses. Within the Verticillium genus, which comprises important phytopathogenic fungi, a group-I intron was previously identified in the SSU-rRNA (18S) gene of only V. longisporum. In this work, we aimed at elucidating the SSU-located intron distribution in V. dahliae and other Verticillium species, and the assessment of heterogeneity regarding intron content among rDNA repeats of fungal strains. Using conserved PCR primers for the amplification of the SSU gene, a structurally similar novel intron (sub-group IC1) was detected in only a few V. dahliae isolates. However, when intron-specific primers were used for the screening of a diverse collection of Verticillium isolates that originally failed to produce intron-containing SSU amplicons, most were found to contain one or both intron types, at variable rDNA repeat numbers. This marked heterogeneity was confirmed with qRT-PCR by testing rDNA copy numbers (varying from 39 to 70 copies per haploid genome) and intron copy ratios in selected isolates. Our results demonstrate that (a) IC1 group-I introns are not specific to V. longisporum within the Verticillium genus, (b) V. dahliae isolates of vegetative compatibility groups (VCGs) 4A and 6, which bear the novel intron at most of their rDNA repeats, are closely related, and (c) there is considerable intra-genomic heterogeneity for the presence or absence of introns among the ribosomal repeats. These findings underline that distributions of introns in the highly heterogeneous repetitive rDNA complex should always be verified with sensitive methods to avoid misleading conclusions for the phylogeny of fungi and other organisms.
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Affiliation(s)
- Ioannis A Papaioannou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
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Otálora MA, Aragón G, Martínez I, Wedin M. Cardinal characters on a slippery slope – A re-evaluation of phylogeny, character evolution, and evolutionary rates in the jelly lichens (Collemataceae s. str). Mol Phylogenet Evol 2013; 68:185-98. [DOI: 10.1016/j.ympev.2013.04.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 03/26/2013] [Accepted: 04/02/2013] [Indexed: 10/27/2022]
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9
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Leavitt SD, Esslinger TL, Divakar PK, Lumbsch HT. Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions. BMC Evol Biol 2012; 12:176. [PMID: 22963132 PMCID: PMC3499221 DOI: 10.1186/1471-2148-12-176] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/30/2012] [Indexed: 01/22/2023] Open
Abstract
Background Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescent-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. Results We found that divergence estimates, from both concatenated gene tree and coalescent-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. Conclusions Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.
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Porter TM, Golding GB. Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS One 2012; 7:e35749. [PMID: 22558215 PMCID: PMC3338786 DOI: 10.1371/journal.pone.0035749] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/23/2012] [Indexed: 12/13/2022] Open
Abstract
Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50-100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys.
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Hafez M, Iranpour M, Mullineux ST, Sethuraman J, Wosnitza KM, Lehn P, Kroeker J, Loewen PC, Reid J, Hausner G. Identification of group I introns within the SSU rDNA gene in species of Ceratocystiopsis and related taxa. Fungal Biol 2012; 116:98-111. [DOI: 10.1016/j.funbio.2011.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 11/28/2022]
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12
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Lumbsch HT, Leavitt SD. Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0123-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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13
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Kelly LJ, Hollingsworth PM, Coppins BJ, Ellis CJ, Harrold P, Tosh J, Yahr R. DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. THE NEW PHYTOLOGIST 2011; 191:288-300. [PMID: 21434928 DOI: 10.1111/j.1469-8137.2011.03677.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
• Efforts are currently underway to establish a standard DNA barcode region for fungi; we tested the utility of the internal transcribed spacer (ITS) of nuclear ribosomal DNA for DNA barcoding in lichen-forming fungi by sampling diverse species across eight orders. • Amplification of the ITS region (ITS1-5.8S-ITS2) was conducted for 351 samples, encompassing 107, 55 and 28 species, genera and families, respectively, of lichenized fungi. We assessed the ability of the entire ITS vs the ITS2 alone to discriminate between species in a taxonomic dataset (members of the genus Usnea) and a floristic dataset. • In the floristic dataset, 96.3% of sequenced samples could be assigned to the correct species using ITS or ITS2; a barcode gap for ITS is present in 92.1% of species. Although fewer species have a barcode gap in the taxonomic dataset (73.3% with ITS and 68.8% with ITS2), up to 94.1% of samples were assigned to the correct species using BLAST. • While discrimination between the most closely related species will remain challenging, our results demonstrate the potential to identify a high percentage of specimens to the correct species, and the remainder to the correct genus, when using DNA barcoding in a floristic context.
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Affiliation(s)
- Laura J Kelly
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
- Present address: Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Peter M Hollingsworth
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Brian J Coppins
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Christopher J Ellis
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Paul Harrold
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - James Tosh
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Rebecca Yahr
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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14
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Martinson HG. An active role for splicing in 3′-end formation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:459-70. [DOI: 10.1002/wrna.68] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Nelsen MP, Gargas A. Dissociation and horizontal transmission of codispersing lichen symbionts in the genus Lepraria (Lecanorales: Stereocaulaceae). THE NEW PHYTOLOGIST 2007; 177:264-275. [PMID: 17944828 DOI: 10.1111/j.1469-8137.2007.02241.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Lichenized fungi of the genus Lepraria lack ascomata and conidiomata, and symbionts codisperse by soredia. Here, it is determined whether algal symbionts associated with Lepraria are monophyletic, and whether fungal and algal phylogenies are congruent, both of which are indicative of a long-term, continuous association between symbionts. The internal transcribed spacer (ITS) and part of the actin type I locus were sequenced from algae associated with Lepraria, and the fungal ITS and mitochondrial small subunit (mtSSU) were sequenced from fungal symbionts. Phylogenetic analyses tested for monophyly of algal symbionts and congruence between algal and fungal phylogenies. Algae associated with Lepraria were not monophyletic, and identical algae associated with different Lepraria individuals and species. Algal and fungal phylogenies were not congruent, suggesting a lack of strict codiversification. This study suggests that associations between symbionts are not strictly maintained over evolutionary time. The ability to switch partners may provide benefits similar to genetic recombination, which may have helped this lineage persist.
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Affiliation(s)
- Matthew P Nelsen
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706-1381, USA
- Present address: Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931-1295, USA
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Hofstetter V, Miadlikowska J, Kauff F, Lutzoni F. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: A case study of the Lecanoromycetes (Ascomycota). Mol Phylogenet Evol 2007; 44:412-26. [PMID: 17207641 DOI: 10.1016/j.ympev.2006.10.016] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Accepted: 10/10/2006] [Indexed: 11/24/2022]
Abstract
The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.
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Gutiérrez G, Blanco O, Divakar PK, Lumbsch HT, Crespo A. Patterns of group I intron presence in nuclear SSU rDNA of the Lichen family Parmeliaceae. J Mol Evol 2007; 64:181-95. [PMID: 17200806 DOI: 10.1007/s00239-005-0313-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2005] [Accepted: 10/09/2006] [Indexed: 10/23/2022]
Abstract
Group I introns are commonly reported within nuclear SSU ribosomal DNA of eukaryotic micro-organisms, especially in lichen-forming fungi. We have studied the primary and secondary structure of 70 new nuclear SSU rDNA group I introns of Parmeliaceae (Ascomycota: Lecanorales) and compared them with those available in databases, covering more than 60 species. The analyzed samples of Parmeliaceae fell into two groups, one having an intron at the 1506 site and another lacking this one but having another at the 1516 or 1521 position. Introns at the 1521 position seem to be transposed from 1516 sites. Introns at the 1516 position were similar in structure to ones previously reported at this site and known from other lecanoralean fungi, while those at the 1506 position showed structural differences and no similar introns are known from related fungi. The study of the distribution of group I introns within a large monophyletic ensemble of fungi has revealed an unexpected correlation between intron types and ecological and geographical parameters. The introns at the 1516 position occurred in mainly arctic, boreal, and temperate lichens, while those at position 1506 were present in mainly tropical and subtropical to oceanic mild-temperate taxa. Further, the 1516 introns occurred in genera with few distributed species that could represent older taxa, while the 1506 ones were mainly in species-rich genera that could be of recent speciation, as many species have wide distribution areas. The transition between two different environments has been accompanied by a change in introns gained and lost.
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Affiliation(s)
- Gabriel Gutiérrez
- Departamento de Ciencias Ambientales, Universidad Pablo de Olavide, Sevilla, Spain
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