1
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Petipas RH, Antoch AA, Eaker AA, Kehlet-Delgado H, Friesen ML. Back to the future: Using herbarium specimens to isolate nodule-associated bacteria. Ecol Evol 2024; 14:e11719. [PMID: 39011130 PMCID: PMC11246978 DOI: 10.1002/ece3.11719] [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: 11/02/2023] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Herbarium specimens are increasingly being used as sources of information to understand the ecology and evolution of plants and their associated microbes. Most studies have used specimens as a source of genetic material using culture-independent approaches. We demonstrate that herbarium specimens can also be used to culture nodule-associated bacteria, opening the possibility of using specimens to understand plant-microbe interactions at new spatiotemporal scales. We used historic and contemporary nodules of a common legume, Medicago lupulina, to create a culture collection. We were able to recover historic bacteria in 15 genera from three specimens (collected in 1950, 2004, and 2015). This work is the first of its kind to isolate historic bacteria from herbarium specimens. Future work should include inoculating plants with historic strains to see if they produce nodules and if they affect plant phenotype and fitness. Although we were unable to recover any Ensifer, the main symbiont of Medicago lupulina, we recovered some other potential nodulating species, as well as many putative growth-promoting bacteria.
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Affiliation(s)
- Renee H Petipas
- Department of Plant Pathology Washington State University Pullman Washington USA
| | - Amanda A Antoch
- Department of Plant Pathology Washington State University Pullman Washington USA
- Department of Microbiology University of Washington Seattle Washington USA
| | - Ashton A Eaker
- Department of Plant Pathology Washington State University Pullman Washington USA
| | - Hanna Kehlet-Delgado
- Department of Plant Pathology Washington State University Pullman Washington USA
| | - Maren L Friesen
- Department of Plant Pathology Washington State University Pullman Washington USA
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2
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Campos PE, Pruvost O, Boyer K, Chiroleu F, Cao TT, Gaudeul M, Baider C, Utteridge TMA, Becker N, Rieux A, Gagnevin L. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nat Commun 2023; 14:4306. [PMID: 37474518 PMCID: PMC10359311 DOI: 10.1038/s41467-023-39950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
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Affiliation(s)
- Paola E Campos
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | | | - Thuy Trang Cao
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
- Herbier national, Muséum national d'Histoire naturelle, CP39, 57 rue Cuvier, 75005, Paris, France
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security, R.E. Vaughan Building (MSIRI Compound), Reduit, 80835, Mauritius
| | | | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- CIRAD, UMR PHIM, Montpellier, France.
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3
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Bradshaw MJ, Carey J, Liu M, Bartholomew HP, Jurick WM, Hambleton S, Hendricks D, Schnittler M, Scholler M. Genetic time traveling: sequencing old herbarium specimens, including the oldest herbarium specimen sequenced from kingdom Fungi, reveals the population structure of an agriculturally significant rust. THE NEW PHYTOLOGIST 2023; 237:1463-1473. [PMID: 36385249 DOI: 10.1111/nph.18622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Sequencing herbarium specimens can be instrumental in answering ecological, evolutionary, and taxonomic inquiries. We developed a protocol for sequencing herbarium specimens of rust fungi (Pucciniales) and proceeded to sequence specimens ranging from 4 to 211 yr old from five different genera. We then obtained sequences from an economically important biological control agent, Puccinia suaveolens, to highlight the potential of sequencing herbarium specimens in an ecological sense and to evaluate the following hypotheses: (1) The population structure of a plant pathogen changes over time, and (2) introduced pathogens are more diverse in their native range. Our efforts resulted in sequences from 87 herbarium specimens that revealed a high level of diversity with a population structure that exhibited spatial-temporal patterns. The specimens sequenced from Europe showed more diversity than the ones from North America, uncovering an invasion pattern likely related to its European native host in North America. Additionally, to the best of our knowledge, the specimen from France collected in c. 1811 is the oldest herbarium specimen sequenced from kingdom Fungi. In conclusion, sequencing old herbarium specimens is an important tool that can be extrapolated to better understand plant-microbe evolution and to evaluate old type specimens to solidify the taxonomy of plant pathogenic fungi.
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Affiliation(s)
- Michael J Bradshaw
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Julie Carey
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Miao Liu
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Holly P Bartholomew
- Food Quality Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Wayne M Jurick
- Food Quality Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Sarah Hambleton
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Dylan Hendricks
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Martin Schnittler
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, 17487, Greifswald, Germany
| | - Markus Scholler
- Staatliches Museum für Naturkunde, Abteilung Biowissenschaften, D-76133, Karlsruhe, Germany
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4
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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5
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Li W, Li Z, Zhang L, Deng X, Zheng Z. Genome Sequence Resource of Xanthomonas citri pv. citri from Formalin-Fixed Citrus Leaves Specimen Showing Canker Lesions Collected in 1982. PLANT DISEASE 2022; 106:304-306. [PMID: 34328361 DOI: 10.1094/pdis-05-21-1100-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xanthomonas citri pv. citri is the causative agent of citrus canker, one of the most devastating diseases threatening global citrus production. Here, we present the genome sequence of X. citri pv. citri strain GD82 from a formalin-fixed citrus leaf specimen showing canker lesions collected in 1982 in Guangdong Province, China. The GD82 genome consisted of 5,197,217 bp with G+C content of 64.8%, along with four circular plasmids: pXAC33 (32,377 bp), pXAC64 (63,972 bp), pXAC47 (47,810 bp), and pGD82.1 (219,560 bp). This is the oldest X. citri pv. citri genome from historical citrus canker specimens in China, which will enrich the current X. citri pv. citri genome database and facilitate genomic evolution research of X. citri pv. citri.
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Affiliation(s)
- Wenting Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Zhenxi Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Ling Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Xiaoling Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Zheng Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
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6
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Rabbee MF, Islam N, Baek KH. Biocontrol of citrus bacterial canker caused by Xanthomonas citri subsp. citri by Bacillus velezensis. Saudi J Biol Sci 2021; 29:2363-2371. [PMID: 35531204 PMCID: PMC9072923 DOI: 10.1016/j.sjbs.2021.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 11/18/2022] Open
Abstract
Microorganisms with biocontrol capabilities against plant pathogens are considered as one of the most promising approaches for healthy crop management. In this study, ethyl acetate extracts of 25 Bacillus strains were investigated for their antagonistic effect on Xanthomonas citri subsp. citri (Xcc), which causes the citrus bacterial canker (CBC) disease. Among them, 21 strains exerted antibacterial activity against wild-type Xcc strains. Based on the strength of the antibacterial activity, nine Bacillus strains were selected for 16S rRNA analysis. 16S rRNA sequence homology revealed that several strains were closely related to B. velezensis, where strains with no antibacterial activity grouped as the soil-associated community of B. amyloliquefaciens. B. velezensis Bv-21 exhibited the highest antibacterial activity against wild type and streptomycin resistant Xcc with inhibition zones of 22.91 ± 0.45 and 20.28 ± 0.53, respectively. Furthermore, B. velezensis Bv-21 strain was tested for biocontrol activity against a streptomycin-resistant XccM4 in detached susceptible citrus leaves. The strain reduced the incidence of CBC by 26.30% and pathogen density of XccM4 by 81.68% over control. The results of the study strongly suggest that B. velezensis can be used as an effective and eco-friendly biocontrol agent either by itself or as an active compound, against both, the wild-type and streptomycin-resistant Xcc.
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Affiliation(s)
- Muhammad Fazle Rabbee
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Nurul Islam
- Soil Resource Development Institute, Regional Office, Rajshahi 6000, Bangladesh
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
- Corresponding author.
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7
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Campos PE, Groot Crego C, Boyer K, Gaudeul M, Baider C, Richard D, Pruvost O, Roumagnac P, Szurek B, Becker N, Gagnevin L, Rieux A. First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence. PLoS Pathog 2021; 17:e1009714. [PMID: 34324594 PMCID: PMC8320980 DOI: 10.1371/journal.ppat.1009714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.
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Affiliation(s)
- Paola E. Campos
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
- Herbier national (P), Muséum national d’Histoire naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound), Agricultural Services, Réduit, Mauritius
| | | | | | - Philippe Roumagnac
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
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8
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Robène I, Maillot-Lebon V, Chabirand A, Moreau A, Becker N, Moumène A, Rieux A, Campos P, Gagnevin L, Gaudeul M, Baider C, Chiroleu F, Pruvost O. Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants. BMC Microbiol 2020; 20:296. [PMID: 33004016 PMCID: PMC7528614 DOI: 10.1186/s12866-020-01972-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/08/2020] [Indexed: 01/07/2023] Open
Abstract
Background Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols. Results Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD95% = 754 CFU ml− 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95% = 5234 CFU ml− 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays. Conclusions We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.
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Affiliation(s)
| | | | - Aude Chabirand
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Aurélie Moreau
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | - Amal Moumène
- Université de La Réunion, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Paola Campos
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | | | - Myriam Gaudeul
- Herbier national (P), Muséum National d'Histoire Naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound) Agricultural Services, Réduit, Mauritius
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9
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Ristaino JB. The Importance of Mycological and Plant Herbaria in Tracking Plant Killers. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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10
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Ferrasa A, Murata MM, Cofre TDCG, Cavallini JS, Peron G, Julião MHM, Belasque J, Ferreira H, Ferro MIT, Leite RP, Penha HA, Carvalho FMS, Varani AM, Herai RH, Ferro JA. CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5979747. [PMID: 33181825 PMCID: PMC7904050 DOI: 10.1093/database/baaa081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/05/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023]
Abstract
Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.
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Affiliation(s)
- Adriano Ferrasa
- Departamento de Informática, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, PR, Brazil.,Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), R. Imaculada Conceição, 1155, 80215-901, Curitiba, PR, Brazil
| | - Mayara M Murata
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.,Diretoria de PÓs-Graduação Stricto Sensu, Universidade Norte do Paraná (UNOPAR), Av. Paris, 675, 86041-100, Londrina, PR, Brazil
| | - Teresa D C G Cofre
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Juliana S Cavallini
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Gustavo Peron
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Maria H M Julião
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo (USP), Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil
| | - Henrique Ferreira
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Av. 24-A, 1515, 13506-900, Rio Claro, SP, Brazil
| | - Maria Inês T Ferro
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Rui P Leite
- Instituto Agronômico do Paraná (IAPAR), Londrina, Rod. Celso Garcia Cid, km 375, 86047-902, Londrina, PR, Brazil
| | - Helen A Penha
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.,Inprenha Biotecnologia e Desenvolvimento Avançado LTDA, Fazenda Lagoinha, Estrada Velha de Taquaritinga, Km 04, 14870-970, Jaboticabal, SP, Brazil
| | - Flávia M S Carvalho
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Alessandro M Varani
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Roberto H Herai
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), R. Imaculada Conceição, 1155, 80215-901, Curitiba, PR, Brazil
| | - Jesus A Ferro
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
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11
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Jeong K, Muñoz-Bodnar A, Arias Rojas N, Poulin L, Rodriguez-R LM, Gagnevin L, Vernière C, Pruvost O, Koebnik R. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri. BMC Genomics 2019; 20:917. [PMID: 31791238 PMCID: PMC6889575 DOI: 10.1186/s12864-019-6267-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/06/2019] [Indexed: 12/26/2022] Open
Abstract
Background Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.
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Affiliation(s)
- Kwanho Jeong
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Alejandra Muñoz-Bodnar
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Current address: Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Lucie Poulin
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Laboratoire de Biologie et de Pathologie Végétales, Université de Nantes, Nantes, France
| | - Luis Miguel Rodriguez-R
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lionel Gagnevin
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,CIRAD, UMR PVBMT, 97410, Saint Pierre, La Réunion, France
| | - Christian Vernière
- CIRAD, UMR PVBMT, 97410, Saint Pierre, La Réunion, France.,CIRAD, UMR BGPI, 34398, Montpellier, France
| | | | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.
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12
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Wolkis D, Deans S. Picking from the Past in Preparation for a Pest: Seed Banks Outperform Herbaria as Sources of Preserved 'Ōhi'a Seed. Biopreserv Biobank 2019; 17:583-590. [PMID: 31429591 DOI: 10.1089/bio.2019.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Seed banks serve the purpose of maintaining germplasm for ex situ species preservation. Herbarium vouchers may be a viable source of unique and/or additional seeds for restoration as they can sometimes be from larger and more representative populations compared with seed banks. Rapid 'ōhi'a death (ROD) has emerged as a serious threat against Hawaii's most iconic and foundational forest tree (Metrosideros spp.), and seed banking has been identified as an important strategy in preserving the genetic diversity of 'ōhi'a. With respect to 'ōhi'a we ask the following: (1) what is the long-term viability of 'ōhi'a seeds stored in herbarium conditions, (2) how do herbarium curation practices affect seed viability, and (3) how long do seeds survive using conventional storage methods? We placed fresh 'ōhi'a seeds in a herbarium dryer (57°C/5% relative humidity) for 5 days, freezer (-18°C/95% RH) for 2 weeks, and dryer then freezer, and compared against fresh control seeds. Seeds were harvested from a chronosequence of herbarium specimens, withdrawn from conventional storage conditions up to 3.75 and 6.5 years before experiments began, and germination assessed. There was no difference in the proportion germinated among treatments and control testing for herbarium entry (p = 0.56). Although no seeds from herbarium specimens germinated, freshly collected dried and frozen seeds germinated at a level equivalent to the control (p = 0.76). For seeds stored using conventional storage methods at 3.75 and 6.5 years, germination was equivalent to freshly harvested seeds. This suggests that seeds can survive the extreme climate conditions necessary to enter herbaria, but lose viability after storage at ambient conditions in 4 years or less. Although 'ōhi'a seeds may be plentiful in herbaria, we recommend using seeds deposited into seed banks using conventional storage methods for orthodox seeds for postdisturbance restoration, and to combat ROD.
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Affiliation(s)
- Dustin Wolkis
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaii
| | - Susan Deans
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaii.,Department of Plant Science, Chicago Botanic Garden, Glencoe, Illinois.,Plant Biology and Conservation, Northwestern University, Evanston, Illinois
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New Ca. Liberibacter psyllaurous haplotype resurrected from a 49-year-old specimen of Solanum umbelliferum: a native host of the psyllid vector. Sci Rep 2019; 9:9530. [PMID: 31267035 PMCID: PMC6606623 DOI: 10.1038/s41598-019-45975-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/18/2019] [Indexed: 11/29/2022] Open
Abstract
Over the last century, repeated emergence events within the Candidatus Liberibacter taxon have produced pathogens with devastating effects. Presently, our knowledge of Ca. Liberibacter diversity, host associations, and interactions with vectors is limited due to a focus on studying this taxon within crops. But to understand traits associated with pathogen emergence it is essential to study pathogen diversity in wild vegetation as well. Here, we explore historical native host plant associations and diversity of the cosmopolitan species, Ca. L. psyllaurous, also known as Ca. L. solanacearum, which is associated with psyllid yellows disease and zebra chip disease, especially in potato. We screened tissue from herbarium samples of three native solanaceous plants collected near potato-growing regions throughout Southern California over the last century. This screening revealed a new haplotype of Ca. L. psyllaurous (G), which, based on our sampling, has been present in the U.S. since at least 1970. Phylogenetic analysis of this new haplotype suggests that it may be closely related to a newly emerged North American haplotype (F) associated with zebra chip disease in potatoes. Our results demonstrate the value of herbarium sampling for discovering novel Ca. Liberibacter haplotypes not previously associated with disease in crops.
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14
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Daru BH, Bowman EA, Pfister DH, Arnold AE. A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170395. [PMID: 30455213 PMCID: PMC6282087 DOI: 10.1098/rstb.2017.0395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2018] [Indexed: 12/22/2022] Open
Abstract
Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome (Andromeda polifolia and Ledum palustre subsp. groenlandicum, Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years. We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
| | | | - Donald H Pfister
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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15
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Cernava T, Berg G, Grube M. High Life Expectancy of Bacteria on Lichens. MICROBIAL ECOLOGY 2016; 72:510-3. [PMID: 27464604 PMCID: PMC5023722 DOI: 10.1007/s00248-016-0818-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/06/2016] [Indexed: 05/20/2023]
Abstract
Self-sustaining lichen symbioses potentially can become very old, sometimes even thousands of years in nature. In the joint structures, algal partners are sheltered between fungal structures that are externally colonized by bacterial communities. With this arrangement lichens survive long periods of drought, and lichen thalli can be revitalized even after decades of dry storage in a herbarium. To study the effects of long-term ex situ storage on viability of indigenous bacterial communities we comparatively studied herbarium-stored material of the lung lichen, Lobaria pulmonaria. We discovered that a significant fraction of the lichen-associated bacterial community survives herbarium storage of nearly 80 years, and living bacteria can still be found in even older material. As the bacteria reside in the upper surface layers of the lichen material, we argue that the extracellular polysaccharides of lichens contribute to superior life expectancy of bacteria. Deeper understanding of underlying mechanisms could provide novel possibilities for biotechnological applications.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010, Graz, Austria.
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Hartung JS, Roy A, Fu S, Shao J, Schneider WL, Brlansky RH. History and Diversity of Citrus leprosis virus Recorded in Herbarium Specimens. PHYTOPATHOLOGY 2015; 105:1277-84. [PMID: 25961338 DOI: 10.1094/phyto-03-15-0064-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Leprosis refers to two diseases of citrus that present similar necrotic local lesions, often surrounded by chlorotic haloes on citrus. Two distinct viruses are associated with this disease, one that produces particles primarily in the nucleus of infected plant cells (Citrus leprosis virus nuclear type [CiLV-N]; Dichorhavirus) and another type that produces particles in the cytoplasm of infected plant cells (Citrus leprosis virus cytoplasmic type [CiLV-C]; Cilevirus). Both forms are transmitted by Brevipalpid mites and have bipartite, single-stranded, RNA genomes. CiLV-C and CiLV-N are present in South and Central America and as far north as parts of Mexico. Although leprosis disease was originally described from Florida, it disappeared from there in the 1960s. The United States Department of Agriculture-Agricultural Research Service maintains preserved citrus specimens identified at inspection stations 50 or more years ago with symptoms of citrus leprosis. We isolated RNA from these samples and performed degradome sequencing. We obtained nearly full-length genome sequences of both a typical CiLV-C isolate intercepted from Argentina in 1967 and a distinct CiLV-N isolate obtained in Florida in 1948. The latter is a novel form of CiLV-N, not known to exist anywhere in the world today. We have also documented the previously unreported presence of CiLV-N in Mexico in the mid-20th century.
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Affiliation(s)
- John S Hartung
- First and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Molecular Plant Pathology Laboratory, Beltsville, MD 20705; second and fifth authors: USDA-ARS Foreign Diseases and Weed Sciences Research Unit, Fort Detrick, MD; third author: USDA-ARS Molecular Plant Pathology Laboratory and Southwest University, Citrus Research Institute, Chongqing, China 400715; and sixth author: University of Florida, Citrus Research and Education Center, Lake Alfred 33850
| | - Avijit Roy
- First and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Molecular Plant Pathology Laboratory, Beltsville, MD 20705; second and fifth authors: USDA-ARS Foreign Diseases and Weed Sciences Research Unit, Fort Detrick, MD; third author: USDA-ARS Molecular Plant Pathology Laboratory and Southwest University, Citrus Research Institute, Chongqing, China 400715; and sixth author: University of Florida, Citrus Research and Education Center, Lake Alfred 33850
| | - Shimin Fu
- First and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Molecular Plant Pathology Laboratory, Beltsville, MD 20705; second and fifth authors: USDA-ARS Foreign Diseases and Weed Sciences Research Unit, Fort Detrick, MD; third author: USDA-ARS Molecular Plant Pathology Laboratory and Southwest University, Citrus Research Institute, Chongqing, China 400715; and sixth author: University of Florida, Citrus Research and Education Center, Lake Alfred 33850
| | - Jonathan Shao
- First and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Molecular Plant Pathology Laboratory, Beltsville, MD 20705; second and fifth authors: USDA-ARS Foreign Diseases and Weed Sciences Research Unit, Fort Detrick, MD; third author: USDA-ARS Molecular Plant Pathology Laboratory and Southwest University, Citrus Research Institute, Chongqing, China 400715; and sixth author: University of Florida, Citrus Research and Education Center, Lake Alfred 33850
| | - William L Schneider
- First and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Molecular Plant Pathology Laboratory, Beltsville, MD 20705; second and fifth authors: USDA-ARS Foreign Diseases and Weed Sciences Research Unit, Fort Detrick, MD; third author: USDA-ARS Molecular Plant Pathology Laboratory and Southwest University, Citrus Research Institute, Chongqing, China 400715; and sixth author: University of Florida, Citrus Research and Education Center, Lake Alfred 33850
| | - Ronald H Brlansky
- First and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Molecular Plant Pathology Laboratory, Beltsville, MD 20705; second and fifth authors: USDA-ARS Foreign Diseases and Weed Sciences Research Unit, Fort Detrick, MD; third author: USDA-ARS Molecular Plant Pathology Laboratory and Southwest University, Citrus Research Institute, Chongqing, China 400715; and sixth author: University of Florida, Citrus Research and Education Center, Lake Alfred 33850
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17
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Pruvost O, Magne M, Boyer K, Leduc A, Tourterel C, Drevet C, Ravigné V, Gagnevin L, Guérin F, Chiroleu F, Koebnik R, Verdier V, Vernière C. A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage. PLoS One 2014; 9:e98129. [PMID: 24897119 PMCID: PMC4045669 DOI: 10.1371/journal.pone.0098129] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 04/28/2014] [Indexed: 11/18/2022] Open
Abstract
MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).
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Affiliation(s)
- Olivier Pruvost
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Maxime Magne
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Karine Boyer
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Alice Leduc
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Christophe Tourterel
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France
- Institut de Génétique et Microbiologie, UMR 8621, Université de Paris-Sud, Orsay, France
- Institut de Génétique et Microbiologie, UMR 8621, CNRS, Orsay, France
| | - Christine Drevet
- Institut de Génétique et Microbiologie, UMR 8621, Université de Paris-Sud, Orsay, France
- Institut de Génétique et Microbiologie, UMR 8621, CNRS, Orsay, France
| | - Virginie Ravigné
- UMR Biologie et Génétiques des Interactions Plante-Parasite (BGPI), CIRAD, Montpellier, France
| | - Lionel Gagnevin
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Fabien Guérin
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Université de la Réunion, Saint Pierre, La Réunion, France
| | - Frédéric Chiroleu
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Ralf Koebnik
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France
| | - Valérie Verdier
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France
| | - Christian Vernière
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
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Culley TM. Why vouchers matter in botanical research. APPLICATIONS IN PLANT SCIENCES 2013; 1:apps1300076. [PMID: 25202501 PMCID: PMC4103463 DOI: 10.3732/apps.1300076] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 09/23/2013] [Indexed: 05/25/2023]
Abstract
What is a voucher and why is it important in research? As a preserved specimen of an identified taxon deposited in a permanent and accessible storage facility, the voucher serves as the supporting material for published studies of the taxon and ensures that the science is repeatable. Vouchers are crucial in authenticating the taxonomy of an organism, as a tool for identifying localities of the taxon, and for additional taxonomic, genetic, ecological, and/or environmental research.
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Ye G, Hong N, Zou LF, Zou HS, Zakria M, Wang GP, Chen GY. tale-Based Genetic Diversity of Chinese Isolates of the Citrus Canker Pathogen Xanthomonas citri subsp. citri. PLANT DISEASE 2013; 97:1187-1194. [PMID: 30722424 DOI: 10.1094/pdis-12-12-1201-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Pathotype A of Xanthomonas citri subsp. citri, the cause of citrus bacterial canker (CBC), is assumed to have originated in southern China. PthA, a type III secreted transcriptional activator-like effector (TALE), is a major pathogenicity determinant in X. citri subsp. citri. To investigate the diversity of X. citri subsp. citri in China, genomic and plasmid DNA of 105 X. citri subsp. citri isolates, collected from nine citrus-growing provinces of China, were digested by BamHI and hybridized with an internal repeat region of pthA. Strains were classified into 14 different genotypes (designated A to N) based on the number and size of pthA homologues. Genotypes B and G represented 19 and 62% of the isolate collection, respectively. Genotypes J and L lacked pthA or a pthA-hybridizing fragment and were less virulent on grapefruit (C. paradisi) and sweet orange (C. sinensis) compared with strains containing pthA or a pthA homologue. The virulence of genotypes J and L was increased when the wild-type pthA was introduced. Genotype I, which was isolated from sweet orange in Jiangxi province, caused typical canker symptoms and may contain a novel pthA-like gene. To our knowledge, this is the first description of genetic diversity in Chinese CBC strains based on tale gene analysis.
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Affiliation(s)
- Gang Ye
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Li-Fang Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua-Song Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Zakria
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guo-Ping Wang
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University
| | - Gong-You Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University
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Wang Y, Liu JH. Exogenous treatment with salicylic acid attenuates occurrence of citrus canker in susceptible navel orange (Citrus sinensis Osbeck). JOURNAL OF PLANT PHYSIOLOGY 2012; 169:1143-9. [PMID: 22658220 DOI: 10.1016/j.jplph.2012.03.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 03/20/2012] [Accepted: 03/27/2012] [Indexed: 05/22/2023]
Abstract
Citrus canker caused by Xanthomonas axonopodis pv. citri (Xac) is a devastating bacterial disease threatening the citrus industry. Salicylic acid (SA) plays a key role in plant defense response to biotic stress, but information is scarce concerning the application of SA to enhancing Xac resistance. In the present research attempts were made to investigate how exogenous application of SA influenced canker disease outbreak in navel orange (Citrus sinensis). Exogenously applied SA at 0.25 mM significantly enhanced the endogenous free and bound SA, particularly the latter. Upon exposure to Xac, lower disease incidence rate and smaller lesion sites were observed in the samples pre-treated with SA, accompanied by repression of bacterial growth at the lesion sites. Concurrent with the augmented disease resistance, SA-treated leaves had higher H₂O₂ level and smaller stomata apertures before or after Xac infection when compared with their counterparts pre-treated with water (control). SA treatment elevated the activities of phenylalanine ammonia-lyase and β-1,3-glucanase, but only the latter was higher in the SA-treated samples after Xac infection. In addition, mRNA levels of two pathogenesis-related genes, CsCHI and CsPR4A, were higher in the SA-treated samples relative to the control. Taken together, our results strongly suggest that the exogenously applied SA has evoked a cascade of physiological and molecular events that function singly or in concert to confer resistance to Xac invasion.
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Affiliation(s)
- Yin Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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Abstract
We report the 5.1-Mb genome sequence of Xanthomonas citri pv. mangiferaeindicae strain LMG 941, the causal agent of bacterial black spot in mango. Apart from evolutionary studies, the draft genome will be a valuable resource for the epidemiological studies and quarantine of this phytopathogen.
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Abstract
We report the 4.94-Mb genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859, the causal agent of bacterial leaf blight disease in pomegranate. The draft genome will aid in comparative genomics, epidemiological studies, and quarantine of this devastating phytopathogen.
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Jaciani FJ, Ferro JA, Ferro MIT, Vernière C, Pruvost O, Belasque J. Genetic Diversity of a Brazilian Strain Collection of Xanthomonas citri subsp. citri Based on the Type III Effector Protein Genes. PLANT DISEASE 2012; 96:193-203. [PMID: 30731808 DOI: 10.1094/pdis-04-11-0357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Exclusion and eradication or management based on an integrated approach with less susceptible varieties, copper-based bactericides, and windbreaks are the two main strategies used to prevent or control citrus canker. Field tolerance or resistance to citrus canker is not found in the most important commercial sweet orange cultivars, and pathogen-derived resistance has been developed and applied in different crops to obtain resistant genotypes to plant pathogens. We describe the development of DNA primers and probes based on the type III effector genes avrXacE1, avrXacE2, avrXacE3, avrBs2, pthA4, hpaF, and XAC3090 (leucine rich protein), and their application in the evaluation of the genetic diversity of the pathogen. A total of 49 haplotypes were identified in 157 strains by Southern blot analysis. No genetic polymorphism was detected by BOX elements - and enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) analysis, nor with the genes avrBs2, XAC3090, and hpaF. Nei's genetic diversity indexes varied from 0.65 to 0.96 for subcollections of the pathogen. One or few haplotypes were most frequent in the strain collection, but several haplotypes were represented by solely one or few strains. The PthA4 probe resulted in the higher number of haplotypes identified in the Brazilian subcollections. Greater variation in the frequency of haplotypes occurred within subcollections (93.7%) than among subcollections. Only some haplotypes were genetically distant from all others, especially those originated from Rio Grande do Sul and Santa Catarina states. These bacterial effectors are widely spread in the collections and are useful for a better understanding of the host-pathogen interaction and the search for resistance genes in host and nonhost plants.
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Affiliation(s)
- F J Jaciani
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ. Estadual Paulista, Campus de Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - J A Ferro
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ. Estadual Paulista, Campus de Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - M I T Ferro
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ. Estadual Paulista, Campus de Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - C Vernière
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7, chemin de l'Irat, 97410 Saint Pierre, Réunion, France
| | - O Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7, chemin de l'Irat, 97410 Saint Pierre, Réunion, France
| | - J Belasque
- Fundo de Defesa da Citricultura, Araraquara, SP, Brazil
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The blossoming of plant archaeogenetics. Ann Anat 2012; 194:146-56. [DOI: 10.1016/j.aanat.2011.03.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 03/25/2011] [Accepted: 03/25/2011] [Indexed: 11/19/2022]
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Pruvost O, Vernière C, Vital K, Guérin F, Jouen E, Chiroleu F, Ah-You N, Gagnevin L. Insertion sequence- and tandem repeat-based genotyping techniques for Xanthomonas citri pv. mangiferaeindicae. PHYTOPATHOLOGY 2011; 101:887-893. [PMID: 21323466 DOI: 10.1094/phyto-11-10-0304] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Molecular fingerprinting techniques that have the potential to identify or subtype bacteria at the strain level are needed for improving diagnosis and understanding of the epidemiology of pathogens such as Xanthomonas citri pv. mangiferaeindicae, which causes mango bacterial canker disease. We developed a ligation-mediated polymerase chain reaction targeting the IS1595 insertion sequence as a means to differentiate pv. mangiferaeindicae from the closely related pv. anacardii (responsible for cashew bacterial spot), which has the potential to infect mango but not to cause significant disease. This technique produced weakly polymorphic fingerprints composed of ≈70 amplified fragments per strain for a worldwide collection of X. citri pv. mangiferaeindicae but produced no or very weak amplification for pv. anacardii strains. Together, 12 tandem repeat markers were able to subtype X. citri pv. mangiferaeindicae at the strain level, distinguishing 231 haplotypes from a worldwide collection of 299 strains. Multilocus variable number of tandem repeats analysis (MLVA), IS1595-ligation-mediated polymerase chain reaction, and amplified fragment length polymorphism showed differences in discriminatory power and were congruent in describing the diversity of this strain collection, suggesting low levels of recombination. The potential of the MLVA scheme for molecular epidemiology studies of X. citri pv. mangiferaeindicae is discussed.
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Affiliation(s)
- O Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7, chemin de l'Irat, 97410 Saint Pierre, Réunion, France.
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Hawkins SA, Park B, Poole GH, Gottwald T, Windham WR, Lawrence KC. Detection of citrus Huanglongbing by Fourier transform infrared-attenuated total reflection spectroscopy. APPLIED SPECTROSCOPY 2010; 64:100-3. [PMID: 20132604 DOI: 10.1366/000370210790572043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Citrus Huanglongbing (HLB, also known as citrus greening disease) was discovered in Florida in 2005 and is spreading rapidly amongst the citrus growing regions of the state. Detection via visual symptoms of the disease is not a long-term viable option. New techniques are being developed to test for the disease in its earlier presymptomatic stages. Fourier transform infrared-attenuated total reflection (FT-IR-ATR) spectroscopy is a candidate for rapid, inexpensive, early detection of the disease. The mid-infrared region of the spectrum reveals dramatic changes that take place in the infected leaves when compared to healthy non-infected leaves. The carbohydrates that give rise to peaks in the 900-1180 cm(-1) range are reliable in distinguishing leaves from infected plants versus non-infected plants. A model based on chemometrics was developed using the spectra from 179 plants of known disease status. This model then correctly predicted the status of >95% of the plants tested.
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Affiliation(s)
- Samantha A Hawkins
- US Department of Agriculture-Agricultural Research Service Russell Research Center, 950 College Station Rd, Athens, Georgia 30605, USA.
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Ngoc LBT, Vernière C, Belasque JJ, Vital K, Boutry S, Gagnevin L, Pruvost O. Ligation-mediated PCR, a fast and reliable technique for insertion sequence-based typing of Xanthomonas citri pv. citri. FEMS Microbiol Lett 2009; 288:33-9. [PMID: 18771421 DOI: 10.1111/j.1574-6968.2008.01331.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Asiatic citrus canker, caused by Xanthomonas citri pv. citri, is a major disease threatening citrus crops throughout the world. The most common methods for strain differentiation of this pathogen are repetitive element sequence-based PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE), using rare-cutting restriction enzyme analysis. We developed a ligation-mediated PCR targeting three insertion sequences (IS-LM-PCR) present as several copies in the genome of the fully sequenced strain 306 of X. citri pv. citri. This technique amplifies DNA fragments between an insertion sequence element and an MspI restriction site. The analysis of strains can be conducted within 24 h, starting from very small amounts of bacterial DNA, which makes IS-LM-PCR much less labor-intensive than PFGE. We used IS-LM-PCR to analyze a collection of 66 strains of X. citri pv. citri from around the world. The overall reproducibility of IS-LM-PCR reached 98% in this data set and its discriminatory power was markedly superior than rep-PCR. We suggest that IS-LM-PCR could be used for the global surveillance of non-epidemiologically related strains of X. citri pv. citri.
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Bui TNL, Vernière C, Jarne P, Brisse S, Guérin F, Boutry S, Gagnevin L, Pruvost O. From local surveys to global surveillance: three high-throughput genotyping methods for epidemiological monitoring of Xanthomonas citri pv. citri pathotypes. Appl Environ Microbiol 2009; 75:1173-84. [PMID: 19088309 PMCID: PMC2643580 DOI: 10.1128/aem.02245-08] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 12/10/2008] [Indexed: 01/18/2023] Open
Abstract
Asiatic citrus canker is a major disease worldwide, and its causal agent, Xanthomonas citri pv. citri, is listed as a quarantine organism in many countries. Analysis of the molecular epidemiology of this bacterium is hindered by a lack of molecular typing techniques suitable for surveillance and outbreak investigation. We report a comparative evaluation of three typing techniques, amplified fragment length polymorphism (AFLP) analysis, insertion sequence ligation-mediated PCR (IS-LM-PCR) typing, and multilocus variable-number tandem-repeat analysis (MLVA), with 234 strains originating from Asia, the likely center of origin of the pathogen, and reference strains of pathotypes A, A*, and A(w), which differ in host range. The typing techniques were congruent in describing the diversity of this strain collection, suggesting that the evolution pattern of the bacterium may be clonal. Based on a hierarchical analysis of molecular variance, the AFLP method best described the genetic variation found among pathotypes whereas MLVA best described the variation found among individual strains from the same countries or groups of neighboring countries. IS-LM-PCR data suggested that the transposition of insertion sequences in the genome of X. citri pv. citri occurs rarely enough not to disturb the phylogenetic signal. This technique may be useful for the global surveillance of non-epidemiologically related strains. Although pathological characteristics of strains could be most often predicted from genotyping data, we report the occurrence in the Indian peninsula of strains genetically related to pathotype A* strains but with a host range similar to that of pathotype A, which makes the classification of this bacterium even more complicated.
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Affiliation(s)
- Thi Ngoc Lan Bui
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7 chemin de l'Irat, 97410 Saint Pierre, La Réunion, France
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Telle S, Thines M. Amplification of cox2 (approximately 620 bp) from 2 mg of up to 129 years old herbarium specimens, comparing 19 extraction methods and 15 polymerases. PLoS One 2008; 3:e3584. [PMID: 18974835 PMCID: PMC2572190 DOI: 10.1371/journal.pone.0003584] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 10/07/2008] [Indexed: 11/18/2022] Open
Abstract
During the past years an increasing number of studies have focussed on the use of herbarium specimens for molecular phylogenetic investigations and several comparative studies have been published. However, in the studies reported so far usually rather large amounts of material (typically around 100 mg) were sampled for DNA extraction. This equals an amount roughly equivalent to 8 cm(2) of a medium thick leaf. For investigating the phylogeny of plant pathogens, such large amounts of tissue are usually not available or would irretrievably damage the specimens. Through systematic comparison of 19 DNA extraction protocols applied to only 2 mg of infected leaf tissue and testing 15 different DNA polymerases, we could successfully amplify a mitochondrial DNA region (cox2; approximately 620 bp) from herbarium specimens well over a hundred years old. We conclude that DNA extraction and the choice of DNA polymerase are crucial factors for successful PCR amplification from small samples of historic herbarium specimens. Through a combination of suitable DNA extraction protocols and DNA polymerases, only a fraction of the preserved plant material commonly used is necessary for successful PCR amplification. This facilitates the potential use of a far larger number of preserved specimens for molecular phylogenetic investigation and provides access to a wealth of genetic information in preserved in specimens deposited in herbaria around the world without reducing their scientific or historical value.
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Affiliation(s)
- Sabine Telle
- University of Hohenheim, Institute of Botany 210, Stuttgart, Germany
| | - Marco Thines
- University of Hohenheim, Institute of Botany 210, Stuttgart, Germany
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