1
|
Feau N, Herath P, Hamelin RC. DNA-Barcoding Identification of Plant Pathogens for Disease Diagnostics. Methods Mol Biol 2023; 2659:37-49. [PMID: 37249883 DOI: 10.1007/978-1-0716-3159-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The accurate identification of plant pathogens is a critical step to prevent their spread and attenuate their impact. Among the wide range of methods available, DNA-barcoding, i.e., the identification of an organism through the PCR amplification and sequencing of a single locus, remains one of the most straightforward and accurate plant-pathogen identification techniques that can be used in a generic molecular biology lab. This chapter provides a detailed protocol for the isolation of genomic DNA of fungal and oomycete pathogens from fresh field samples and the amplification and sequencing of the internal transcribed spacer (ITS) locus for DNA-barcoding purpose. Amendments to the protocol are provided to help in resolving issues related to the analysis of complicated samples and to the lack of species resolution that can be encountered with ITS barcodes.
Collapse
Affiliation(s)
- Nicolas Feau
- Canadian Forest Service, Pacific Forestry Centre, Natural Resources Canada, Victoria, BC, Canada.
| | - Padmini Herath
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Richard C Hamelin
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
2
|
Penaud B, Laurent B, Milhes M, Noüs C, Ehrenmann F, Dutech C. SNP4OrphanSpecies: A bioinformatics pipeline to isolate molecular markers for studying genetic diversity of orphan species. Biodivers Data J 2022; 10:e85587. [PMID: 36761595 PMCID: PMC9848450 DOI: 10.3897/bdj.10.e85587] [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: 04/20/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022] Open
Abstract
Background For several decades, an increase in disease or pest emergences due to anthropogenic introduction or environmental changes has been recorded. This increase leads to serious threats to the genetic and species diversity of numerous ecosystems. Many of these events involve species with poor or no genomic resources (called here "orphan species"). This lack of resources is a serious limitation to our understanding of the origin of emergent populations, their ability to adapt to new environments and to predict future consequences to biodiversity. Analyses of genetic diversity are an efficient method to obtain this information rapidly, but require available polymorphic genetic markers. New information We developed a generic bioinformatics pipeline to rapidly isolate such markers with the goal for the pipeline to be applied in studies of invasive taxa from different taxonomic groups, with a special focus on forest fungal pathogens and insect pests. This pipeline is based on: 1) an automated de novo genome assembly obtained from shotgun whole genome sequencing using paired-end Illumina technology; 2) the isolation of single-copy genes conserved in species related to the studied emergent organisms; 3) primer development for multiplexed short sequences obtained from these conserved genes. Previous studies have shown that intronic regions of these conserved genes generally contain several single nucleotide polymorphisms within species. The pipeline's functionality was evaluated with sequenced genomes of five invasive or expanding pathogen and pest species in Europe (Armillariaostoyae (Romagn.) Herink 1973, Bursaphelenchusxylophilus Steiner & Buhrer 1934, Sphaeropsissapinea (fr.) Dicko & B. Sutton 1980, Erysiphealphitoides (Griffon & Maubl.) U. Braun & S. Takam. 2000, Thaumetopoeapityocampa Denis & Schiffermüller, 1775). We successfully isolated several pools of one hundred short gene regions for each assembled genome, which can be amplified in multiplex. The bioinformatics pipeline is user-friendly and requires little computational resources. This easy-to-set-up and run method for genetic marker identification will be useful for numerous laboratories studying biological invasions, but with limited resources and expertise in bioinformatics.
Collapse
Affiliation(s)
- Benjamin Penaud
- BIOGECO, INRAE, Univ. Bordeaux, 33610 Cestas, FranceBIOGECO, INRAE, Univ. Bordeaux33610 CestasFrance
| | - Benoit Laurent
- BIOGECO, INRAE, Univ. Bordeaux, 33610 Cestas, FranceBIOGECO, INRAE, Univ. Bordeaux33610 CestasFrance
| | - Marine Milhes
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, FranceINRAE, US 1426, GeT-PlaGe, GenotoulCastanet-TolosanFrance
| | - Camille Noüs
- Laboratoire Cogitamus, Bordeaux, FranceLaboratoire CogitamusBordeauxFrance
| | - François Ehrenmann
- BIOGECO, INRAE, Univ. Bordeaux, 33610 Cestas, FranceBIOGECO, INRAE, Univ. Bordeaux33610 CestasFrance
| | - Cyril Dutech
- BIOGECO, INRAE, Univ. Bordeaux, 33610 Cestas, FranceBIOGECO, INRAE, Univ. Bordeaux33610 CestasFrance
| |
Collapse
|
3
|
Detection and Molecular Phylogenetic-Morphometric Characterization of Rhizoctonia tuliparum, Causal Agent of Gray Bulb Rot of Tulips and Bulbous Iris. J Fungi (Basel) 2022; 8:jof8020163. [PMID: 35205917 PMCID: PMC8880388 DOI: 10.3390/jof8020163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
Gray bulb rot of tulips and bulbous iris is caused by the soil-borne fungal pathogen, Rhizoctonia tuliparum (Rtul). Sclerotia present in infected bulbs, as well as overwintering sclerotia in soil and field debris, are the primary sources of infection. A method for accurate and sensitive detection of Rtul from soil and infected bulbs, and estimation of inoculum threshold levels, is needed for the management of disease caused by this pathogen. We designed a unique set of primers targeting the ITS2 region of the Rtul genome and developed a highly sensitive quantitative PCR (qPCR)-based method for Rtul identification using these primers, where the threshold of detection was approximately 1 fg Rtul DNA. The assay was more sensitive with sclerotia collected from the field (natural) than with those grown in the lab, and more sensitive with natural-light than natural-dark sclerotia. Also, the detection method was more sensitive when sclerotia were extracted from soil than from bulb tissue. The qPCR method was highly specific, as no PCR amplification was detected when genomic DNA from 62 non-Rtul Rhizoctonia isolates from a wide range of anastomosis groups were tested. To understand the evolutionary relationships and genomic diversity of Rtul, we performed phylogenetics of the ITS1-5.8S-ITS2 region and ITS2-molecular morphometric characterization (MMC) of Rtul isolates. The three Rtul isolates whose ITS sequences were available in GenBank formed a distinct phylogenetic clade with Ceratobasidium anceps as the nearest relative. Furthermore, MMC analysis revealed genetic divergence among these three Rtul isolates.
Collapse
|
4
|
Shaker Al-Rubaiee Z, Salh Hussin M, Baho S. Evolutionary Relationship and the Sequence Similarities among Different Fungal Species Infecting Birds Captured from Different Areas in Denmark. ARCHIVES OF RAZI INSTITUTE 2022; 77:491-496. [PMID: 35891731 PMCID: PMC9288641 DOI: 10.22092/ari.2021.356858.1929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 12/19/2021] [Indexed: 06/15/2023]
Abstract
Fungal diseases are the common cause of death in wild animals and birds of prey. This study was designed to investigate the development of fungal infections among wild birds in Denmark. In this study, fungal samples were isolated from such sources as Barn swallows' feathers, White stork, and birds of prey. The fungal species were isolated by direct culture of feathers on SD Agar with chloramphenicol and incubated at 28±2ºC. The fungal genomic DNA was isolated from each species, PCR reaction was performed, and the resulting fragments of the 18S rRNA DNA were sequenced and used for identification. A comparison between the resulting fragments was made to find out the percentage of similarity among the different fungal species. The multiple sequence alignment showed percentages of similarities ranging from 39% to 99%. To sum up, the 18S rRNA DNA sequence has been evolved dramatically even within the same species, while still conserved in others. It is a useful tool to be used for the identification of fungal species as it reduces time. Moreover, according to the results, there were no comprehensive high homology percentages among the species infecting the same bird.
Collapse
Affiliation(s)
- Z Shaker Al-Rubaiee
- Biological Department, College of Science, Mustansiriya University, Baghdad, Iraq
| | - M Salh Hussin
- Biological Department, College of Science, Mustansiriya University, Baghdad, Iraq
| | - S Baho
- Biological Department, College of Science, Mustansiriya University, Baghdad, Iraq
| |
Collapse
|
5
|
Han Y, Guo C, Guan X, McMinn A, Liu L, Zheng G, Jiang Y, Liang Y, Shao H, Tian J, Wang M. Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench. MICROBIAL ECOLOGY 2022; 83:34-47. [PMID: 33811505 DOI: 10.1007/s00248-021-01747-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.
Collapse
Affiliation(s)
- Yuye Han
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Xuran Guan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Lu Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guiliang Zheng
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| |
Collapse
|
6
|
Nagel JH, Wingfield MJ, Slippers B. Next-generation sequencing provides important insights into the biology and evolution of the Botryosphaeriaceae. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
7
|
Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles. Sci Rep 2021; 11:16441. [PMID: 34385515 PMCID: PMC8361139 DOI: 10.1038/s41598-021-95776-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
The genus Chaenomeles has long been considered an important ornamental, herbal and cash crop and is widely cultivated in East Asia. Traditional studies of Chaenomeles mainly focus on evolutionary relationships at the phenotypic level. In this study, we conducted RNA-seq on 10 Chaenomeles germplasms supplemented with one outgroup species, Docynia delavayi (D. delavayi), on the Illumina HiSeq2500 platform. After de novo assemblies, we generated from 40,084 to 49,571 unigenes for each germplasm. After pairwise comparison of the orthologous sequences, 9,659 orthologues within the 11 germplasms were obtained, with 6,154 orthologous genes identified as single-copy genes. The phylogenetic tree was visualized to reveal evolutionary relationships for these 11 germplasms. GO and KEGG analyses were performed for these common single-copy genes to compare their functional similarities and differences. Selective pressure analysis based on 6,154 common single-copy genes revealed that 45 genes were under positive selection. Most of these genes are involved in building the plant disease defence system. A total of 292 genes containing simple sequence repeats (SSRs) were used to develop SSR markers and compare their functions in secondary metabolism pathways. Finally, 10 primers were chosen as SSR marker candidates for Chaenomeles germplasms by comprehensive standards. Our research provides a new methodology and reference for future related research in Chaenomeles and is also useful for improvement, breeding and selection projects in other related species.
Collapse
|
8
|
Wang Z, Liu Y, Wang T, Decock C, Chu B, Zheng Q, Lu Q, Zhang X. Grosmannia tibetensis, a new ophiostomatoid fungus associated with Orthotomicus sp. (Coleoptera) in Tibetan subalpine forests. MYCOSCIENCE 2020. [DOI: 10.1016/j.myc.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Csikós A, Németh MZ, Frenkel O, Kiss L, Váczy KZ. A Fresh Look at Grape Powdery Mildew ( Erysiphe necator) A and B Genotypes Revealed Frequent Mixed Infections and Only B Genotypes in Flag Shoot Samples. PLANTS 2020; 9:plants9091156. [PMID: 32906683 PMCID: PMC7570353 DOI: 10.3390/plants9091156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 11/25/2022]
Abstract
Erysiphe necator populations, causing powdery mildew of grapes, have a complex genetic structure. Two genotypes, A and B, were identified in most vineyards across the world on the basis of fixed single nucleotide polymorphisms (SNPs) in several DNA regions. It was hypothesized that A populations overwinter as mycelia in grapevine buds, giving rise to so-called flag shoots in spring, and are more sensitive to fungicides than B populations, which overwinter as ascospores and become widespread later in the season. Other studies concluded that the biological significance of these genotypes is unclear. In the spring of 2015, there was a unique opportunity to collect E. necator samples from flag shoots in Hungary. The same grapevines were sampled in summer and autumn as well. A total of 182 samples were genotyped on the basis of β-tubulin (TUB2), nuclear ribosomal DNA (nrDNA) intergenic spacer (IGS), and internal transcribed spacer (ITS) sequences. Genotypes of 56 samples collected in 2009–2011 were used for comparison. Genotype A was not detected at all in spring, and was present in only 19 samples in total, mixed with genotype B, and sometimes with another frequently found genotype, designated as B2. These results did not support the hypothesis about temporal isolation of the two genotypes and indicated that these are randomly distributed in vineyards.
Collapse
Affiliation(s)
- Anett Csikós
- Food and Wine Research Institute, Eszterházy Károly University, H-3300 Eger, Hungary;
| | - Márk Z. Németh
- Plant Protection Institute, Centre for Agricultural Research, H-1525 Budapest, Hungary; (M.Z.N.); (L.K.)
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan 50250, Israel;
| | - Levente Kiss
- Plant Protection Institute, Centre for Agricultural Research, H-1525 Budapest, Hungary; (M.Z.N.); (L.K.)
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba 4350, Australia
| | - Kálmán Zoltán Váczy
- Food and Wine Research Institute, Eszterházy Károly University, H-3300 Eger, Hungary;
- Correspondence:
| |
Collapse
|
10
|
Jactel H, Desprez-Loustau ML, Battisti A, Brockerhoff E, Santini A, Stenlid J, Björkman C, Branco M, Dehnen-Schmutz K, Douma JC, Drakulic J, Drizou F, Eschen R, Franco JC, Gossner MM, Green S, Kenis M, Klapwijk MJ, Liebhold AM, Orazio C, Prospero S, Robinet C, Schroeder M, Slippers B, Stoev P, Sun J, van den Dool R, Wingfield MJ, Zalucki MP. Pathologists and entomologists must join forces against forest pest and pathogen invasions. NEOBIOTA 2020. [DOI: 10.3897/neobiota.58.54389] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The world’s forests have never been more threatened by invasions of exotic pests and pathogens, whose causes and impacts are reinforced by global change. However, forest entomologists and pathologists have, for too long, worked independently, used different concepts and proposed specific management methods without recognising parallels and synergies between their respective fields. Instead, we advocate increased collaboration between these two scientific communities to improve the long-term health of forests.
Our arguments are that the pathways of entry of exotic pests and pathogens are often the same and that insects and fungi often coexist in the same affected trees. Innovative methods for preventing invasions, early detection and identification of non-native species, modelling of their impact and spread and prevention of damage by increasing the resistance of ecosystems can be shared for the management of both pests and diseases.
We, therefore, make recommendations to foster this convergence, proposing in particular the development of interdisciplinary research programmes, the development of generic tools or methods for pest and pathogen management and capacity building for the education and training of students, managers, decision-makers and citizens concerned with forest health.
Collapse
|
11
|
An easy and robust method for isolation and validation of single-nucleotide polymorphic markers from a first Erysiphe alphitoides draft genome. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01580-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
12
|
Smith RL, Sawbridge T, Mann R, Kaur J, May TW, Edwards J. Rediscovering an old foe: Optimised molecular methods for DNA extraction and sequencing applications for fungarium specimens of powdery mildew (Erysiphales). PLoS One 2020; 15:e0232535. [PMID: 32401807 PMCID: PMC7219758 DOI: 10.1371/journal.pone.0232535] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/16/2020] [Indexed: 11/18/2022] Open
Abstract
The purpose of this study was to identify a reliable DNA extraction protocol to use on 25-year-old powdery mildew specimens from the reference collection VPRI in order to produce high quality sequences suitable to address taxonomic phylogenetic questions. We tested 13 extraction protocols and two library preparation kits and found the combination of the E.Z.N.A.® Forensic DNA kit for DNA extraction and the NuGen Ovation® Ultralow System library preparation kit was the most suitable for this purpose.
Collapse
Affiliation(s)
- Reannon L. Smith
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Australia
- * E-mail:
| | - Tim Sawbridge
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Australia
| | - Ross Mann
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
| | - Jatinder Kaur
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
| | - Tom W. May
- Royal Botanic Gardens Victoria, Melbourne, Australia
| | - Jacqueline Edwards
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Australia
| |
Collapse
|
13
|
Kulik T, Bilska K, Żelechowski M. Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA. Int J Mol Sci 2020; 21:E2645. [PMID: 32290169 PMCID: PMC7177237 DOI: 10.3390/ijms21072645] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.
Collapse
Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| |
Collapse
|
14
|
Jin Y, Zhou J, Zhou J, Hu M, Zhang Q, Kong N, Ren H, Liang L, Yue J. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status. Biol Direct 2020; 15:6. [PMID: 32131884 PMCID: PMC7057466 DOI: 10.1186/s13062-020-0258-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer This article was reviewed by Dr. Xianwen Ren.
Collapse
Affiliation(s)
- Yuan Jin
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jianglin Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jing Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Qi Zhang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Na Kong
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,Anhui University, Hefei, 230039, Anhui, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
| | - Long Liang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,Anhui University, Hefei, 230039, Anhui, China.
| | - Junjie Yue
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
| |
Collapse
|
15
|
Luchi N, Ioos R, Santini A. Fast and reliable molecular methods to detect fungal pathogens in woody plants. Appl Microbiol Biotechnol 2020; 104:2453-2468. [PMID: 32006049 PMCID: PMC7044139 DOI: 10.1007/s00253-020-10395-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/10/2020] [Accepted: 01/19/2020] [Indexed: 12/11/2022]
Abstract
Plant diseases caused by pathogenic microorganisms represent a serious threat to plant productivity, food security, and natural ecosystems. An effective framework for early warning and rapid response is a crucial element to mitigate or prevent the impacts of biological invasions of plant pathogens. For these reasons, detection tools play an important role in monitoring plant health, surveillance, and quantitative pathogen risk assessment, thus improving best practices to mitigate and prevent microbial threats. The need to reduce the time of diagnosis has prompted plant pathologists to move towards more sensitive and rapid methods such as molecular techniques. Considering prevention to be the best strategy to protect plants from diseases, this review focuses on fast and reliable molecular methods to detect the presence of woody plant pathogens at early stage of disease development before symptoms occur in the host. A harmonized pool of novel technical, methodological, and conceptual solutions is needed to prevent entry and establishment of new diseases in a country and mitigate the impact of both invasive and indigenous organisms to agricultural and forest ecosystem biodiversity and productivity.
Collapse
Affiliation(s)
- Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, 10, I-50019, Sesto Fiorentino (Firenze), Italy.
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Unit of Mycology, Domaine de Pixérécourt, 54220, Malzéville, France
| | - Alberto Santini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, 10, I-50019, Sesto Fiorentino (Firenze), Italy
| |
Collapse
|
16
|
Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera. PLoS One 2020; 15:e0221742. [PMID: 32023247 PMCID: PMC7001964 DOI: 10.1371/journal.pone.0221742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/28/2019] [Indexed: 12/18/2022] Open
Abstract
Wood and wood products can harbor microorganisms that can raise phytosanitary concerns in countries importing or exporting these products. To evaluate the efficacy of wood treatment on the survival of microorganisms of phytosanitary concern the method of choice is to grow microbes in petri dishes for subsequent identification. However, some plant pathogens are difficult or impossible to grow in axenic cultures. A molecular methodology capable of detecting living fungi and fungus-like organisms in situ can provide a solution. RNA represents the transcription of genes and can become rapidly unstable after cell death, providing a proxy measure of viability. We designed and used RNA-based molecular diagnostic assays targeting genes essential to vital processes and assessed their presence in wood colonized by fungi and oomycetes through reverse transcription and real-time polymerase chain reaction (PCR). A stability analysis was conducted by comparing the ratio of mRNA to gDNA over time following heat treatment of mycelial cultures of the Oomycete Phytophthora ramorum and the fungus Grosmannia clavigera. The real-time PCR results indicated that the DNA remained stable over a period of 10 days post treatment in heat-treated samples, whereas mRNA could not be detected after 24 hours for P. ramorum or 96 hours for G. clavigera. Therefore, this method provides a reliable way to evaluate the viability of these pathogens and offers a potential way to assess the effectiveness of existing and emerging wood treatments. This can have important phytosanitary impacts on assessing both timber and non-timber forest products of commercial value in international wood trade.
Collapse
|
17
|
Ahmed Y, Hubert J, Fourrier-Jeandel C, Dewdney MM, Aguayo J, Ioos R. A Set of Conventional and Multiplex Real-Time PCR Assays for Direct Detection of Elsinoë fawcettii, E. australis, and Pseudocercospora angolensis in Citrus Fruits. PLANT DISEASE 2019; 103:345-356. [PMID: 30566843 DOI: 10.1094/pdis-05-18-0798-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Elsinoë fawcettii, E. australis, and Pseudocercospora angolensis are causal agents of citrus scab and spot diseases. The three pathogens are listed as quarantine pests in many countries and are subject to phytosanitary measures to prevent their entry. Diagnosis of these diseases based on visual symptoms is problematic, as they could be confused with other citrus diseases. Isolation of E. fawcettii, E. australis, and P. angolensis from infected tissues is challenging because they grow slowly on culture media. This study developed rapid and specific detection tools for the in planta detection of these pathogens, using either conventional PCR or one-tube multiplex real-time PCR. Primers and hybridization probes were designed to target the single-copy protein-coding gene MS204 for E. fawcettii and E. australis and the translation elongation factor (Tef-1α) gene for P. angolensis. The specificity of the assays was evaluated by testing against DNA extracted from a large number of isolates (102) collected from different citrus-growing areas in the world and from other hosts. The newly described species E. citricola was not included in the specificity test due to its unavailability from the CBS collection. The detection limits of conventional PCR for the three pathogens were 100, 100, and 10 pg μl-1 gDNA per reaction for E. fawcettii, E. australis, and P. angolensis, respectively. The quadruplex qPCR was fully validated assessing the following performance criteria: sensitivity, specificity, repeatability, reproducibility, and robustness. The quadruplex real-time PCR proved to be highly sensitive, detecting as low as 243, 241, and 242 plasmidic copies (pc) μl-1 of E. fawcettii, E. australis, and P. angolensis, respectively. Sensitivity and specificity of this quadruplex assay were further confirmed using 176 naturally infected citrus samples collected from Ethiopia, Cameroon, the United States, and Australia. The quadruplex assay developed in this study is robust, cost-effective, and capable of high-throughput detection of the three targets directly from citrus samples. This new detection tool will substantially reduce the turnaround time for reliable species identification and allow rapid response and appropriate action.
Collapse
Affiliation(s)
- Yosra Ahmed
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France; and Agricultural Research Center, Plant Pathology Research Institute, Giza- Egypt
| | - Jacqueline Hubert
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France
| | - Céline Fourrier-Jeandel
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France
| | - Megan M Dewdney
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Jaime Aguayo
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France
| | - Renaud Ioos
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France
| |
Collapse
|
18
|
Banos S, Lentendu G, Kopf A, Wubet T, Glöckner FO, Reich M. A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms. BMC Microbiol 2018; 18:190. [PMID: 30458701 PMCID: PMC6247509 DOI: 10.1186/s12866-018-1331-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups. RESULTS We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides. CONCLUSIONS The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.
Collapse
Affiliation(s)
- Stefanos Banos
- Molecular Ecology, Institute of Ecology, FB02, University of Bremen, Leobener Str. 2, 28359, Bremen, Germany
| | - Guillaume Lentendu
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Anna Kopf
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,Present address: Department of Community Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Frank Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
| | - Marlis Reich
- Molecular Ecology, Institute of Ecology, FB02, University of Bremen, Leobener Str. 2, 28359, Bremen, Germany.
| |
Collapse
|
19
|
Feau N, Beauseigle S, Bergeron MJ, Bilodeau GJ, Birol I, Cervantes-Arango S, Dhillon B, Dale AL, Herath P, Jones SJ, Lamarche J, Ojeda DI, Sakalidis ML, Taylor G, Tsui CK, Uzunovic A, Yueh H, Tanguay P, Hamelin RC. Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. PeerJ 2018; 6:e4392. [PMID: 29492338 PMCID: PMC5825881 DOI: 10.7717/peerj.4392] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.
Collapse
Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Inanc Birol
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Sandra Cervantes-Arango
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Braham Dhillon
- Department of Plant Pathology, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- FPInnovations, Vancouver, BC, Canada
| | - Padmini Herath
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Steven J.M. Jones
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Josyanne Lamarche
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Dario I. Ojeda
- Department of Biology Unit of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Monique L. Sakalidis
- Department of Plant, Soil & Microbial Sciences and Department of Forestry, Michigan State University, East Lansing, MI, United States of America
| | - Greg Taylor
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Clement K.M. Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Hesther Yueh
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- Foresterie et géomatique, Institut de Biologie Intégrative des Systèmes, Laval University, Quebec city, Quebec, Canada
| |
Collapse
|
20
|
Dornburg A, Townsend JP, Wang Z. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. ADVANCES IN GENETICS 2017; 100:1-47. [PMID: 29153398 DOI: 10.1016/bs.adgen.2017.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.
Collapse
Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, United States
| | | | - Zheng Wang
- Yale University, New Haven, CT, United States.
| |
Collapse
|
21
|
Reich M, Labes A. How to boost marine fungal research: A first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry. Mar Genomics 2017; 36:57-75. [PMID: 29031541 DOI: 10.1016/j.margen.2017.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/22/2017] [Accepted: 09/23/2017] [Indexed: 12/30/2022]
Abstract
Marine fungi have attracted attention in recent years due to increased appreciation of their functional role in ecosystems and as important sources of new natural products. The concomitant development of various "omic" technologies has boosted fungal research in the fields of biodiversity, physiological ecology and natural product biosynthesis. Each of these research areas has its own research agenda, scientific language and quality standards, which have so far hindered an interdisciplinary exchange. Inter- and transdisciplinary interactions are, however, vital for: (i) a detailed understanding of the ecological role of marine fungi, (ii) unlocking their hidden potential for natural product discovery, and (iii) designing access routes for biotechnological production. In this review and opinion paper, we describe the two different "worlds" of marine fungal natural product chemists and marine fungal molecular ecologists. The individual scientific approaches and tools employed are summarised and explained, and enriched with a first common glossary. We propose a strategy to find a multidisciplinary approach towards a comprehensive view on marine fungi and their chemical potential.
Collapse
Affiliation(s)
- Marlis Reich
- University of Bremen, BreMarE, NW2 B3320, Leobener Str. 5, D-28359 Bremen, Germany.
| | - Antje Labes
- Flensburg University of Applied Sciences, Kanzleistr. 91-93, D-24943 Flensburg, Germany.
| |
Collapse
|
22
|
Desprez-Loustau ML, Massot M, Feau N, Fort T, de Vicente A, Torés JA, Ortuño DF. Further Support of Conspecificity of Oak and Mango Powdery Mildew and First Report of Erysiphe quercicola and Erysiphe alphitoides on Mango in Mainland Europe. PLANT DISEASE 2017; 101:1086-1093. [PMID: 30682963 DOI: 10.1094/pdis-01-17-0116-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mango leaves and inflorescences infected by powdery mildew in southern Spain were analyzed using multigene sequencing (ITS + 4 single-copy coding genes) to identify the causal agent. Erysiphe quercicola was detected in 97% out of 140 samples, collected in six different orchards in the Malaga region. Among these, a small proportion also yielded E. alphitoides (8% of all samples) and E. alphitoides was found alone in 3% of samples. A phylogenetic approach was completed by cross inoculations between oak and mango, which led to typical symptoms, supporting the conspecificity of oak and mango powdery mildews. To our knowledge, this is the first report of E. quercicola and E. alphitoides causing powdery mildew on mango trees in mainland Spain, and thus mainland Europe, based on unequivocal phylogenetic and biological evidence. Our study thus confirmed the broad host range of both E. quercicola and E. alphitoides. These results have practical implications in terms of the demonstrated ability for host range expansion in powdery mildews. They also open interesting prospects to the elucidation of molecular mechanisms underlying the ability to infect single versus multiple and unrelated host plants since these two closely related powdery mildew species belong to a small clade with both generalist and specialist powdery mildews.
Collapse
Affiliation(s)
| | - Marie Massot
- UMR 1202 BIOGECO, INRA, Univ Bordeaux, 33610 Cestas, France
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, British Columbia, The University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Tania Fort
- UMR 1202 BIOGECO, INRA, Univ Bordeaux, 33610 Cestas, France
| | - Antonio de Vicente
- Instituto de Horticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, 29071, Málaga, Spain
| | - Juan Antonio Torés
- Instituto de Horticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Algarrobo-Costa, 29750, Málaga, Spain
| | - Dolores Fernández Ortuño
- Instituto de Horticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, 29071, Málaga, Spain; and Instituto de Horticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Algarrobo-Costa, 29750, Málaga, Spain
| |
Collapse
|
23
|
Marçais B, Piou D, Dezette D, Desprez-Loustau ML. Can Oak Powdery Mildew Severity be Explained by Indirect Effects of Climate on the Composition of the Erysiphe Pathogenic Complex? PHYTOPATHOLOGY 2017; 107:570-579. [PMID: 28026998 DOI: 10.1094/phyto-07-16-0268-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Coinfection by several pathogens is increasingly recognized as an important feature in the epidemiology and evolution of plant fungal pathogens. Oak mildew is induced by two closely related Erysiphe invasive species (Erysiphe alphitoides and E. quercicola) which differ in their mode of overwintering. We investigated how climate influences the co-occurrence of the two species in oak young stands and whether this is important for the disease epidemiology. We studied the frequency of flag-shoots (i.e., shoots developing from infected buds, usually associated with E. quercicola) in 95 oak regenerations over a 6-year period. Additionally, in 2012 and 2013, the oak mildew severity and the two Erysiphe spp. relative frequencies were determined in both spring and autumn in 51 regenerations and 43 1-year-old plantations of oaks. Both the frequency of flag-shoots and the proportion of Erysiphe lesions with E. quercicola presence were related to climate. We showed that survival of E. quercicola was improved after mild winters, with increase of both the flag-shoot frequency and the proportion of Erysiphe lesions with E. quercicola presence in spring. However, disease severity was not related to any complementarity effect between the two Erysiphe spp. causing oak powdery mildew. By contrast, increased E. alphitoides prevalence in spring was associated with higher oak mildew severity in autumn. Our results point out the critical role of between-season transmission and primary inoculum to explain disease dynamics which could be significant in a climate-warming context.
Collapse
Affiliation(s)
- Benoit Marçais
- First author: UMR1136 IAM, INRA, Université de Lorraine, Nancy, F-54280 Champenoux, France; second author: Ministère de l'agriculture, de l'agro-alimentaire et de la forêt DGAL-SDQPV, Département de la Santé des Forêts, 251 rue de Vaugirard, 75732, Paris cedex 15, France; and second, third, and fourth authors: UMR1202 BIOGECO, INRA, University of Bordeaux, F-33610 Cestas, France
| | - Dominique Piou
- First author: UMR1136 IAM, INRA, Université de Lorraine, Nancy, F-54280 Champenoux, France; second author: Ministère de l'agriculture, de l'agro-alimentaire et de la forêt DGAL-SDQPV, Département de la Santé des Forêts, 251 rue de Vaugirard, 75732, Paris cedex 15, France; and second, third, and fourth authors: UMR1202 BIOGECO, INRA, University of Bordeaux, F-33610 Cestas, France
| | - Damien Dezette
- First author: UMR1136 IAM, INRA, Université de Lorraine, Nancy, F-54280 Champenoux, France; second author: Ministère de l'agriculture, de l'agro-alimentaire et de la forêt DGAL-SDQPV, Département de la Santé des Forêts, 251 rue de Vaugirard, 75732, Paris cedex 15, France; and second, third, and fourth authors: UMR1202 BIOGECO, INRA, University of Bordeaux, F-33610 Cestas, France
| | - Marie-Laure Desprez-Loustau
- First author: UMR1136 IAM, INRA, Université de Lorraine, Nancy, F-54280 Champenoux, France; second author: Ministère de l'agriculture, de l'agro-alimentaire et de la forêt DGAL-SDQPV, Département de la Santé des Forêts, 251 rue de Vaugirard, 75732, Paris cedex 15, France; and second, third, and fourth authors: UMR1202 BIOGECO, INRA, University of Bordeaux, F-33610 Cestas, France
| |
Collapse
|
24
|
Dutech C, Labbé F, Capdevielle X, Lung-Escarmant B. Genetic analysis reveals efficient sexual spore dispersal at a fine spatial scale in Armillaria ostoyae, the causal agent of root-rot disease in conifers. Fungal Biol 2017; 121:550-560. [PMID: 28606350 DOI: 10.1016/j.funbio.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/10/2017] [Indexed: 11/24/2022]
Abstract
Armillaria ostoyae (sometimes named Armillaria solidipes) is a fungal species causing root diseases in numerous coniferous forests of the northern hemisphere. The importance of sexual spores for the establishment of new disease centres remains unclear, particularly in the large maritime pine plantations of southwestern France. An analysis of the genetic diversity of a local fungal population distributed over 500 ha in this French forest showed genetic recombination between genotypes to be frequent, consistent with regular sexual reproduction within the population. The estimated spatial genetic structure displayed a significant pattern of isolation by distance, consistent with the dispersal of sexual spores mostly at the spatial scale studied. Using these genetic data, we inferred an effective density of reproductive individuals of 0.1-0.3 individuals/ha, and a second moment of parent-progeny dispersal distance of 130-800 m, compatible with the main models of fungal spore dispersal. These results contrast with those obtained for studies of A. ostoyae over larger spatial scales, suggesting that inferences about mean spore dispersal may be best performed at fine spatial scales (i.e. a few kilometres) for most fungal species.
Collapse
Affiliation(s)
- Cyril Dutech
- BIOGECO, INRA, Univ. Bordeaux, UMR 1202, F-33610 Cestas, France.
| | - Frédéric Labbé
- BIOGECO, INRA, Univ. Bordeaux, UMR 1202, F-33610 Cestas, France
| | | | | |
Collapse
|
25
|
Penselin D, Münsterkötter M, Kirsten S, Felder M, Taudien S, Platzer M, Ashelford K, Paskiewicz KH, Harrison RJ, Hughes DJ, Wolf T, Shelest E, Graap J, Hoffmann J, Wenzel C, Wöltje N, King KM, Fitt BDL, Güldener U, Avrova A, Knogge W. Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses. BMC Genomics 2016; 17:953. [PMID: 27875982 PMCID: PMC5118889 DOI: 10.1186/s12864-016-3299-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/15/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts. RESULTS The genomes of the different Rhynchosporium species were sequenced, assembled and annotated using ab initio gene predictors trained on several fungal genomes as well as on Rhynchosporium expressed sequence tags. Structures of the rDNA regions and genome-wide single nucleotide polymorphisms provided a hypothesis for intra-genus evolution. Homology screening detected core meiotic genes along with most genes crucial for sexual recombination in ascomycete fungi. In addition, a large number of cell wall-degrading enzymes that is characteristic for hemibiotrophic and necrotrophic fungi infecting monocotyledonous hosts were found. Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding for polyketide synthases and non-ribosomal peptide synthetases. Several of these genes are missing from the genome of the closest sequenced relative, the poplar pathogen Marssonina brunnea, and are possibly involved in adaptation to the grass hosts. Most importantly, six species-specific genes coding for protein effectors were identified in R. commune. Their deletion yielded mutants that grew more vigorously in planta than the wild type. CONCLUSION Both cryptic sexuality and secondary metabolites may have contributed to host adaptation. Most importantly, however, the growth-retarding activity of the species-specific effectors suggests that host adaptation of R. commune aims at extending the biotrophic stage at the expense of the necrotrophic stage of pathogenesis. Like other apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host leaves relatively slowly without causing symptoms, reminiscent of the development of endophytic fungi. Rhynchosporium may therefore become an object for studying the mutualism-parasitism transition.
Collapse
Affiliation(s)
- Daniel Penselin
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kirsten
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Marius Felder
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Stefan Taudien
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Matthias Platzer
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Kevin Ashelford
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | | | | | - David J. Hughes
- Applied Bioinformatics, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Thomas Wolf
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Ekaterina Shelest
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Jenny Graap
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Jan Hoffmann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Claudia Wenzel
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany ,Present address: Food Quality and Nutrition, Agroscope, Bern, Switzerland
| | - Nadine Wöltje
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Kevin M. King
- Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Bruce D. L. Fitt
- Biological and Environmental Sciences, University of Hertfordshire, Hatfield, Hertfordshire UK
| | - Ulrich Güldener
- Department of Genome-Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Anna Avrova
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Wolfgang Knogge
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| |
Collapse
|
26
|
Albu S, Schneider RW, Price PP, Doyle VP. Cercospora cf. flagellaris and Cercospora cf. sigesbeckiae Are Associated with Cercospora Leaf Blight and Purple Seed Stain on Soybean in North America. PHYTOPATHOLOGY 2016; 106:1376-1385. [PMID: 27183302 DOI: 10.1094/phyto-12-15-0332-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cercospora kikuchii has long been considered the causal agent of Cercospora leaf blight (CLB) and purple seed stain (PSS) on soybean, but a recent study found C. cf. flagellaris associated with CLB and PSS in Arkansas (United States) and Argentina. Here, we provide a broader perspective on the distribution of C. cf. flagellaris on soybean and alternate hosts within the United States (Arkansas, Louisiana, Mississippi, Missouri, and Kansas). We used a multilocus phylogenetic approach with data from actin, calmodulin, translation elongation factor 1-α, histone 3, the internal transcribed spacer region of rDNA and the mating-type locus to determine that two species, C. cf. flagellaris (200 of 205 isolates) and C. cf. sigesbeckiae (five of 205 isolates), are associated with CLB and PSS in the United States. In our phylogenetic analyses, species-level lineages were generally well-supported, though deeper-level evolutionary relationships remained unresolved, indicating that these genes do not possess sufficient phylogenetic signal to resolve the evolutionary history of Cercospora. We also investigated the potential for sexual reproduction in C. cf. flagellaris in Louisiana by determining the frequency of MAT1-1/MAT1-2 mating-type idiomorphs within the Louisiana population of C. cf. flagellaris. Though the MAT 1-2 idiomorph was significantly more common in our collection, the presence of both mating types suggests the potential for sexual reproduction exists.
Collapse
Affiliation(s)
- S Albu
- First, second, and fourth authors: Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge
- and third author: Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro
| | - R W Schneider
- First, second, and fourth authors: Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge
- and third author: Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro
| | - P P Price
- First, second, and fourth authors: Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge
- and third author: Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro
| | - V P Doyle
- First, second, and fourth authors: Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge
- and third author: Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro
| |
Collapse
|
27
|
Van de Putte K, Nuytinck J, De Crop E, Verbeken A. Lactifluus volemus in Europe: Three species in one--Revealed by a multilocus genealogical approach, Bayesian species delimitation and morphology. Fungal Biol 2015; 120:1-25. [PMID: 26693681 DOI: 10.1016/j.funbio.2015.08.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 08/04/2015] [Accepted: 08/25/2015] [Indexed: 11/26/2022]
Abstract
This study provides morphological and molecular evidence (from nuclear ITS, LSU, and rpb2 DNA sequences) for three previously unrecognized species within the morphospecies Lactifluus volemus from Europe. Phylogenetic species are supported by both a multi-locus tree-based method and Bayesian species delimitation. Lactifluus volemus and Lactifluus oedematopus are provided with a new description, and a third species, Lactifluus subvolemus, is described as new to science. Lactifluus oedematopus can be easily recognized by its short pileipellis hairs. Both L. volemus and L. subvolemus have longer pileipellis hairs and can only be distinguished from each other based on cap colour. Intermediary colour forms, however, occur as well, and cannot be identified as either L. volemus or L. subvolemus without molecular data. Revealing that L. volemus--already considered extinct in the Netherlands and the Belgian Flemish region, and declining in other European countries--is actually a complex of three species that are even more vulnerable to extinction, this study emphasizes the fundamental role of taxonomy in species conservation.
Collapse
Affiliation(s)
- Kobeke Van de Putte
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
| | - Jorinde Nuytinck
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
| | - Eske De Crop
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
| | - Annemieke Verbeken
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
| |
Collapse
|
28
|
Větrovský T, Kolařík M, Žifčáková L, Zelenka T, Baldrian P. Therpb2gene represents a viable alternative molecular marker for the analysis of environmental fungal communities. Mol Ecol Resour 2015; 16:388-401. [DOI: 10.1111/1755-0998.12456] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 07/28/2015] [Accepted: 08/14/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| | - Miroslav Kolařík
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| | - Tomáš Zelenka
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| |
Collapse
|
29
|
Zepeda Mendoza ML, Sicheritz-Pontén T, Gilbert MTP. Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Brief Bioinform 2015; 16:745-58. [PMID: 25673291 PMCID: PMC4570204 DOI: 10.1093/bib/bbv001] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/16/2014] [Indexed: 01/19/2023] Open
Abstract
DNA-based taxonomic and functional profiling is widely used for the characterization of organismal communities across a rapidly increasing array of research areas that include the role of microbiomes in health and disease, biomonitoring, and estimation of both microbial and metazoan species richness. Two principal approaches are currently used to assign taxonomy to DNA sequences: DNA metabarcoding and metagenomics. When initially developed, each of these approaches mandated their own particular methods for data analysis; however, with the development of high-throughput sequencing (HTS) techniques they have begun to share many aspects in data set generation and processing. In this review we aim to define the current characteristics, goals and boundaries of each field, and describe the different software used for their analysis. We argue that an appreciation of the potential and limitations of each method can help underscore the improvements required by each field so as to better exploit the richness of current HTS-based data sets.
Collapse
|
30
|
One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia - Molecular Phylogeny and Evolution of Fungi 2015; 35:242-63. [PMID: 26823635 PMCID: PMC4713107 DOI: 10.3767/003158515x689135] [Citation(s) in RCA: 310] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/03/2015] [Indexed: 12/03/2022]
Abstract
The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1–D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β -tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5–6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
Collapse
|
31
|
Ilves KL, López-Fernández H. A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics. Mol Ecol Resour 2014; 14:802-11. [DOI: 10.1111/1755-0998.12222] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/12/2013] [Accepted: 12/30/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Katriina L. Ilves
- Department of Natural History; Royal Ontario Museum; 100 Queen's Park Toronto Ontario Canada M5S 2C6
| | - Hernán López-Fernández
- Department of Natural History; Royal Ontario Museum; 100 Queen's Park Toronto Ontario Canada M5S 2C6
- Department of Ecology and Evolutionary Biology; University of Toronto; 25 Willcocks Street Toronto Ontario Canada M5S 3B2
| |
Collapse
|
32
|
Gross A, Holdenrieder O, Pautasso M, Queloz V, Sieber TN. Hymenoscyphus pseudoalbidus, the causal agent of European ash dieback. MOLECULAR PLANT PATHOLOGY 2014; 15:5-21. [PMID: 24118686 PMCID: PMC6638674 DOI: 10.1111/mpp.12073] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
UNLABELLED The ascomycete Hymenoscyphus pseudoalbidus (anamorph Chalara fraxinea) causes a lethal disease known as ash dieback on Fraxinus excelsior and Fraxinus angustifolia in Europe. The pathogen was probably introduced from East Asia and the disease emerged in Poland in the early 1990s; the subsequent epidemic is spreading to the entire native distribution range of the host trees. This pathogen profile represents a comprehensive review of the state of research from the discovery of the pathogen and points out knowledge gaps and research needs. TAXONOMY Members of the genus Hymenoscyphus (Helotiales, Leotiomycetidae, Leotiomycetes, Ascomycota) are small discomycetes which form their ascomata on dead plant material. A phylogeny based on the internal transcribed spacers (ITSs) of the rDNA indicated the avirulent Hymenoscyphus albidus, a species native to Europe, as the closest relative of H. pseudoalbidus. SYMPTOMS Hymenoscyphus pseudoalbidus causes necrotic lesions on leaves, twigs and stems, eventually leading to wilting and dieback of girdled shoots. Bark lesions are characterized by a typical dark- to cinnamon-brown discoloration. LIFE CYCLE Hymenoscyphus pseudoalbidus is heterothallic and reproduces sexually on ash petioles in the litter once a year. Ascospores are wind dispersed and infect ash leaves during the summer. The asexual spores only serve as spermatia. TOOLS AND TECHNIQUES The most important techniques for fungal handling, such as detection, isolation, culturing, storage, crossing and ascocarp production, are briefly described. MANAGEMENT Once the disease is established, management is hardly possible. The occurrence of a small fraction of partially tolerant trees constitutes hope for resistance breeding in the future. Healthy-looking trees should be preserved.
Collapse
Affiliation(s)
- Andrin Gross
- Forest Pathology and Dendrology, Institute of Integrative Biology (IBZ), ETH Zurich, 8092, Zurich, Switzerland
| | | | | | | | | |
Collapse
|
33
|
Tonnabel J, Olivieri I, Mignot A, Rebelo A, Justy F, Santoni S, Caroli S, Sauné L, Bouchez O, Douzery EJP. Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach. Mol Phylogenet Evol 2013; 70:37-46. [PMID: 23948865 DOI: 10.1016/j.ympev.2013.07.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 07/12/2013] [Accepted: 07/29/2013] [Indexed: 01/30/2023]
Abstract
Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3' untranslated regions (3'-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers using both public-nucleotide databases and transcriptomic data generated for the group of interest by using next generation sequencing technology. To identify PCR primers for a non-model group, the genus Leucadendron (Proteaceae), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer into the 3'-UTR and the left-hand primer into the coding region. Seven new nuclear markers emerged from this search strategy, three of those included 3'-UTRs. We further compared the phylogenetic potential between our new markers and the ribosomal internal transcribed spacer region (ITS). The sequenced 3'-UTRs yielded higher polymorphism rates than the ITS region did. We did not find strong incongruences with the phylogenetic signal contained in the ITS region and the seven new designed markers but they strongly improved the phylogeny of the genus Leucadendron. Overall, this methodology is efficient in isolating orthologous loci and is valid for any non-model group given the availability of transcriptomic data.
Collapse
Affiliation(s)
- Jeanne Tonnabel
- Université Montpellier 2, CNRS, Institut des Sciences de l'Évolution (UMR 5554), Place Eugène Bataillon, 34095 Montpellier cedex 05, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larsson KH, Townsend J, Grigoriev IV, Hibbett DS. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 2013; 105:1350-73. [PMID: 23935031 DOI: 10.3852/13-003] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000-49 900 00 bp and encode for 12 910-16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.
Collapse
Affiliation(s)
- Manfred Binder
- Biology Department, Clark University, 950 Main Street, Worcester, Massachusetts 01610, and CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
McKinney L, Thomsen I, Kjær E, Bengtsson S, Nielsen L. Rapid invasion by an aggressive pathogenic fungus (Hymenoscyphus pseudoalbidus) replaces a native decomposer (Hymenoscyphus albidus): a case of local cryptic extinction? FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2012.05.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
36
|
β-tubulin paralogue tubC is frequently misidentified as the benA gene in Aspergillus section Nigri taxonomy: primer specificity testing and taxonomic consequences. Persoonia - Molecular Phylogeny and Evolution of Fungi 2012; 29:1-10. [PMID: 23606761 PMCID: PMC3589786 DOI: 10.3767/003158512x658123] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/06/2012] [Indexed: 11/25/2022]
Abstract
β-tubulin (benA, tub-2) and calmodulin (caM) are crucial genes in the taxonomy of Aspergillus section Nigri. Widely used β-tubulin primers are not specific for the benA gene for some taxa and preferentially amplify the tubC paralogue. Sequences of the tubC paralogue are widely combined with benA sequences in recent taxonomical works as well as other works, resulting in incongruent trees. In this study we newly provide benA sequences for several ex-type strains, which were characterised using the tubC gene only. We designed a highly specific forward primer to benA designated Ben2f for use in Aspergillus section Nigri, and tested specificity of numerous primer combinations to β-tubulin paralogs. The primer pairs with the highest specificity to the benA gene and functional across species in section Nigri includes Ben2f/Bt2b, Ben2f/T22 and T10/T22. We also provide tools based on codon usage bias analysis that reliably distinguish both paralogues. Exon/intron arrangement is the next distinctive characteristic, although this tool is not valid outside section Nigri. The species identity of taxa from the A. aculeatus clade used in previous molecular studies was revised using combined molecular data (ITS, benA, caM). These data together with two different PCR-fingerprinting methods indicated that A. japonicus should be treated as a synonym of A. violaceofuscus. Similarly, A. fijiensis is reduced to synonymy with A. brunneoviolaceus.
Collapse
|
37
|
Hartig G, Peters RS, Borner J, Etzbauer C, Misof B, Niehuis O. Oligonucleotide primers for targeted amplification of single-copy nuclear genes in apocritan Hymenoptera. PLoS One 2012; 7:e39826. [PMID: 22768134 PMCID: PMC3387199 DOI: 10.1371/journal.pone.0039826] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/27/2012] [Indexed: 11/19/2022] Open
Abstract
Background Published nucleotide sequence data from the mega-diverse insect order Hymenoptera (sawflies, bees, wasps, and ants) are taxonomically scattered and still inadequate for reconstructing a well-supported phylogenetic tree for the order. The analysis of comprehensive multiple gene data sets obtained via targeted PCR could provide a cost-effective solution to this problem. However, oligonucleotide primers for PCR amplification of nuclear genes across a wide range of hymenopteran species are still scarce. Findings Here we present a suite of degenerate oligonucleotide primer pairs for PCR amplification of 154 single-copy nuclear protein-coding genes from Hymenoptera. These primers were inferred from genome sequence data from nine Hymenoptera (seven species of ants, the honeybee, and the parasitoid wasp Nasonia vitripennis). We empirically tested a randomly chosen subset of these primer pairs for amplifying target genes from six Hymenoptera, representing the families Chrysididae, Crabronidae, Gasteruptiidae, Leucospidae, Pompilidae, and Stephanidae. Based on our results, we estimate that these primers are suitable for studying a large number of nuclear genes across a wide range of apocritan Hymenoptera (i.e., all hymenopterans with a wasp-waist) and of aculeate Hymenoptera in particular (i.e., apocritan wasps with stingers). Conclusions The amplified nucleotide sequences are (a) with high probability from single-copy genes, (b) easily generated at low financial costs, especially when compared to phylogenomic approaches, (c) easily sequenced by means of an additionally provided set of sequencing primers, and (d) suitable to address a wide range of phylogenetic questions and to aid rapid species identification via barcoding, as many amplicons contain both exonic and fast-evolving intronic nucleotides.
Collapse
Affiliation(s)
- Gerrit Hartig
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany
- Universität Münster, Institut für Bioinformatik, Münster, Germany
| | - Ralph S. Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Bonn, Germany
| | - Janus Borner
- Universität Hamburg, Biozentrum Grindel und Zoologisches Museum, Hamburg, Germany
| | - Claudia Etzbauer
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany
| | - Oliver Niehuis
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany
- * E-mail:
| |
Collapse
|
38
|
|
39
|
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]
|