First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence
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 th...
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| Veröffentlicht in: | PLoS pathogens 2021-07, Vol.17 (7), p.e1009714-e1009714 |
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| creator | Campos, Paola E Groot Crego, Clara Boyer, Karine Gaudeul, Myriam Baider, Claudia Richard, Damien Pruvost, Olivier Roumagnac, Philippe Szurek, Boris Becker, Nathalie Gagnevin, Lionel Rieux, Adrien |
| description | 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 19
th
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. |
| doi_str_mv | 10.1371/journal.ppat.1009714 |
| format | Article |
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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 19
th
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.</description><identifier>ISSN: 1553-7374</identifier><identifier>ISSN: 1553-7366</identifier><identifier>EISSN: 1553-7374</identifier><identifier>DOI: 10.1371/journal.ppat.1009714</identifier><identifier>PMID: 34324594</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>19th century ; Agricultural production ; Bacteria ; Bacteria, Pathogenic ; Bayesian analysis ; Biology and Life Sciences ; Calibration ; Canker ; Citrus canker ; Computer and Information Sciences ; Crop diseases ; Damage patterns ; Deoxyribonucleic acid ; Diseases and pests ; DNA ; DNA damage ; Earth Sciences ; Epidemics ; Epidemiology ; Evolutionary genetics ; Genetic aspects ; Genomes ; Genomics ; Herbaria ; History ; Infectious diseases ; Islands ; Life Sciences ; Metagenomics ; Mutation ; Parameter estimation ; Pathogens ; Phylogenetics ; Phylogeny ; Plant diseases ; Single-nucleotide polymorphism ; Slavery ; Virulence ; Virulence factors</subject><ispartof>PLoS pathogens, 2021-07, Vol.17 (7), p.e1009714-e1009714</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Campos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Attribution</rights><rights>2021 Campos et al 2021 Campos et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c672t-e57b45aba77a08e1e7d02147244f1071f267b18c35905314aeb253ba156338c03</citedby><cites>FETCH-LOGICAL-c672t-e57b45aba77a08e1e7d02147244f1071f267b18c35905314aeb253ba156338c03</cites><orcidid>0000-0001-9179-7315 ; 0000-0002-4547-3608 ; 0000-0002-2943-0827 ; 0000-0002-1808-7082 ; 0000-0002-7221-0010 ; 0000-0002-3175-9795 ; 0000-0002-2203-2076 ; 0000-0001-5002-6039 ; 0000-0002-9187-3549 ; 0009-0009-5982-8287</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8320980/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8320980/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://hal.inrae.fr/hal-03327718$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Mackey, David</contributor><creatorcontrib>Campos, Paola E</creatorcontrib><creatorcontrib>Groot Crego, Clara</creatorcontrib><creatorcontrib>Boyer, Karine</creatorcontrib><creatorcontrib>Gaudeul, Myriam</creatorcontrib><creatorcontrib>Baider, Claudia</creatorcontrib><creatorcontrib>Richard, Damien</creatorcontrib><creatorcontrib>Pruvost, Olivier</creatorcontrib><creatorcontrib>Roumagnac, Philippe</creatorcontrib><creatorcontrib>Szurek, Boris</creatorcontrib><creatorcontrib>Becker, Nathalie</creatorcontrib><creatorcontrib>Gagnevin, Lionel</creatorcontrib><creatorcontrib>Rieux, Adrien</creatorcontrib><title>First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence</title><title>PLoS pathogens</title><description>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 19
th
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.</description><subject>19th century</subject><subject>Agricultural production</subject><subject>Bacteria</subject><subject>Bacteria, Pathogenic</subject><subject>Bayesian analysis</subject><subject>Biology and Life Sciences</subject><subject>Calibration</subject><subject>Canker</subject><subject>Citrus canker</subject><subject>Computer and Information Sciences</subject><subject>Crop diseases</subject><subject>Damage patterns</subject><subject>Deoxyribonucleic acid</subject><subject>Diseases and pests</subject><subject>DNA</subject><subject>DNA damage</subject><subject>Earth Sciences</subject><subject>Epidemics</subject><subject>Epidemiology</subject><subject>Evolutionary genetics</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Herbaria</subject><subject>History</subject><subject>Infectious diseases</subject><subject>Islands</subject><subject>Life Sciences</subject><subject>Metagenomics</subject><subject>Mutation</subject><subject>Parameter estimation</subject><subject>Pathogens</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant diseases</subject><subject>Single-nucleotide polymorphism</subject><subject>Slavery</subject><subject>Virulence</subject><subject>Virulence 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patterns</topic><topic>Deoxyribonucleic acid</topic><topic>Diseases and pests</topic><topic>DNA</topic><topic>DNA damage</topic><topic>Earth Sciences</topic><topic>Epidemics</topic><topic>Epidemiology</topic><topic>Evolutionary genetics</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Herbaria</topic><topic>History</topic><topic>Infectious diseases</topic><topic>Islands</topic><topic>Life Sciences</topic><topic>Metagenomics</topic><topic>Mutation</topic><topic>Parameter estimation</topic><topic>Pathogens</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant diseases</topic><topic>Single-nucleotide polymorphism</topic><topic>Slavery</topic><topic>Virulence</topic><topic>Virulence factors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Campos, Paola E</creatorcontrib><creatorcontrib>Groot Crego, Clara</creatorcontrib><creatorcontrib>Boyer, 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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 19
th
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.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>34324594</pmid><doi>10.1371/journal.ppat.1009714</doi><orcidid>https://orcid.org/0000-0001-9179-7315</orcidid><orcidid>https://orcid.org/0000-0002-4547-3608</orcidid><orcidid>https://orcid.org/0000-0002-2943-0827</orcidid><orcidid>https://orcid.org/0000-0002-1808-7082</orcidid><orcidid>https://orcid.org/0000-0002-7221-0010</orcidid><orcidid>https://orcid.org/0000-0002-3175-9795</orcidid><orcidid>https://orcid.org/0000-0002-2203-2076</orcidid><orcidid>https://orcid.org/0000-0001-5002-6039</orcidid><orcidid>https://orcid.org/0000-0002-9187-3549</orcidid><orcidid>https://orcid.org/0009-0009-5982-8287</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1553-7374 |
| ispartof | PLoS pathogens, 2021-07, Vol.17 (7), p.e1009714-e1009714 |
| issn | 1553-7374 1553-7366 1553-7374 |
| language | eng |
| recordid | cdi_plos_journals_2561941100 |
| source | Public Library of Science (PLoS) Journals Open Access; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access |
| subjects | 19th century Agricultural production Bacteria Bacteria, Pathogenic Bayesian analysis Biology and Life Sciences Calibration Canker Citrus canker Computer and Information Sciences Crop diseases Damage patterns Deoxyribonucleic acid Diseases and pests DNA DNA damage Earth Sciences Epidemics Epidemiology Evolutionary genetics Genetic aspects Genomes Genomics Herbaria History Infectious diseases Islands Life Sciences Metagenomics Mutation Parameter estimation Pathogens Phylogenetics Phylogeny Plant diseases Single-nucleotide polymorphism Slavery Virulence Virulence factors |
| title | First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence |
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