{"id":"https://openalex.org/W3029954871","doi":"https://doi.org/10.1016/j.pbi.2020.04.009","title":"The rise and fall of genes: origins and functions of plant pathogen pangenomes","display_name":"The rise and fall of genes: origins and functions of plant pathogen pangenomes","publication_year":2020,"publication_date":"2020-05-29","ids":{"openalex":"https://openalex.org/W3029954871","doi":"https://doi.org/10.1016/j.pbi.2020.04.009","mag":"3029954871","pmid":"https://pubmed.ncbi.nlm.nih.gov/32480355"},"language":"en","primary_location":{"id":"doi:10.1016/j.pbi.2020.04.009","doi":"https://doi.org/10.1016/j.pbi.2020.04.009","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.pbi.2020.04.009","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1369526620300492/pdf","source":{"id":"https://openalex.org/S69957782","display_name":"Current Opinion in Plant Biology","issn_l":"1369-5266","issn":["1369-5266","1879-0356"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-1","medline","norway-1","poland-140","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Current Opinion in Plant Biology","raw_type":"journal-article"},"volume":null,"type":"review","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.sciencedirect.com/science/article/pii/S1369526620300492/pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010495883","display_name":"Thomas Badet","orcid":"https://orcid.org/0000-0001-6130-441X","observed_orcids":["https://orcid.org/0000-0001-6130-441X"]},"institutions":[{"id":"https://openalex.org/I57825437","display_name":"University of Neuch\u00e2tel","ror":"https://ror.org/00vasag41","country_code":"CH","type":"education","lineage":["https://openalex.org/I57825437"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Thomas Badet","raw_affiliation_strings":["Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuch\u00e2tel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuch\u00e2tel, Switzerland","institution_ids":["https://openalex.org/I57825437"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027850387","display_name":"Daniel Croll","orcid":"https://orcid.org/0000-0002-2072-380X","observed_orcids":["https://orcid.org/0000-0002-2072-380X"]},"institutions":[{"id":"https://openalex.org/I57825437","display_name":"University of Neuch\u00e2tel","ror":"https://ror.org/00vasag41","country_code":"CH","type":"education","lineage":["https://openalex.org/I57825437"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Daniel Croll","raw_affiliation_strings":["Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuch\u00e2tel, Switzerland. Electronic address: daniel.croll@unine.ch","Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuch\u00e2tel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-2072-380X","affiliations":[{"raw_affiliation_string":"Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuch\u00e2tel, Switzerland. Electronic address: daniel.croll@unine.ch","institution_ids":["https://openalex.org/I57825437"]},{"raw_affiliation_string":"Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuch\u00e2tel, Switzerland","institution_ids":["https://openalex.org/I57825437"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5027850387"],"corresponding_institution_ids":["https://openalex.org/I57825437"],"apc_list":{"value":4300,"currency":"USD","value_usd":4300},"apc_paid":{"value":4300,"currency":"USD","value_usd":4300},"fwci":1.368,"has_fulltext":true,"cited_by_count":98,"citation_normalized_percentile":{"value":0.79030481,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"56","issue":null,"first_page":"65","last_page":"73"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11578","display_name":"Plant Pathogenic Bacteria Studies","score":0.8378999829292297,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11578","display_name":"Plant Pathogenic Bacteria Studies","score":0.8378999829292297,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10076","display_name":"Plant-Microbe Interactions and Immunity","score":0.054499998688697815,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10825","display_name":"Plant Pathogens and Fungal Diseases","score":0.04560000076889992,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/accessory-genome","display_name":"accessory genome","score":0.7210000157356262},{"id":"https://openalex.org/keywords/core-genome","display_name":"core genome","score":0.8640000224113464},{"id":"https://openalex.org/keywords/effectors","display_name":"effectors","score":0.8700000047683716},{"id":"https://openalex.org/keywords/host-adaptation","display_name":"host adaptation","score":0.6019999980926514}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9272005558013916},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.7811834216117859},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.7691586017608643},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.7290064692497253},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.6501660346984863},{"id":"https://openalex.org/C153991713","wikidata":"https://www.wikidata.org/wiki/Q17142856","display_name":"Niche","level":2,"score":0.6196801066398621},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6135348081588745},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.594890296459198},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.5413517951965332},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.4806198477745056},{"id":"https://openalex.org/C2776914050","wikidata":"https://www.wikidata.org/wiki/Q19597524","display_name":"Host adaptation","level":4,"score":0.4494558870792389},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4359932243824005},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.4334403872489929},{"id":"https://openalex.org/C2779999212","wikidata":"https://www.wikidata.org/wiki/Q7278228","display_name":"R gene","level":4,"score":0.4293835759162903},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40909838676452637},{"id":"https://openalex.org/C93678976","wikidata":"https://www.wikidata.org/wiki/Q4215946","display_name":"Plant disease resistance","level":3,"score":0.2811453342437744},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.1746443808078766},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.0},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010935","descriptor_name":"Plant Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1016/j.pbi.2020.04.009","doi":"https://doi.org/10.1016/j.pbi.2020.04.009","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.pbi.2020.04.009","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1369526620300492/pdf","source":{"id":"https://openalex.org/S69957782","display_name":"Current Opinion in Plant Biology","issn_l":"1369-5266","issn":["1369-5266","1879-0356"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-1","medline","norway-1","poland-140","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Current Opinion in Plant Biology","raw_type":"journal-article"},{"id":"pmid:32480355","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32480355","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Current opinion in plant biology","raw_type":"Journal Article"},{"id":"pmh:oai:HAL:hal-05802463v1","doi":null,"is_oa":false,"landing_page_url":"https://hal.science/hal-05802463","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Current Opinion in Plant Biology, 2020, 56, pp.65-73. &#x27E8;10.1016/j.pbi.2020.04.009&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1016/j.pbi.2020.04.009","doi":"https://doi.org/10.1016/j.pbi.2020.04.009","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.pbi.2020.04.009","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1369526620300492/pdf","source":{"id":"https://openalex.org/S69957782","display_name":"Current Opinion in Plant Biology","issn_l":"1369-5266","issn":["1369-5266","1879-0356"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-1","medline","norway-1","poland-140","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Current Opinion in Plant Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.5365999937057495}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320331806","display_name":"Fondation Pierre Mercier","ror":"https://ror.org/04t8x1s67"},{"id":"https://openalex.org/F4320331997","display_name":"Fondation Pierre Mercier pour la Science","ror":"https://ror.org/042j59742"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3029954871.pdf","grobid_xml":"https://content.openalex.org/works/W3029954871.grobid-xml"},"referenced_works_count":83,"referenced_works":["https://openalex.org/W1963459864","https://openalex.org/W1964353015","https://openalex.org/W1983761774","https://openalex.org/W2036847230","https://openalex.org/W2054562396","https://openalex.org/W2055156321","https://openalex.org/W2056764669","https://openalex.org/W2080924682","https://openalex.org/W2093610003","https://openalex.org/W2099507355","https://openalex.org/W2103569188","https://openalex.org/W2104863787","https://openalex.org/W2107903364","https://openalex.org/W2117536415","https://openalex.org/W2119594582","https://openalex.org/W2140602911","https://openalex.org/W2145928478","https://openalex.org/W2148239117","https://openalex.org/W2153082917","https://openalex.org/W2171209136","https://openalex.org/W2171468101","https://openalex.org/W2179421710","https://openalex.org/W2409013835","https://openalex.org/W2468803195","https://openalex.org/W2493079113","https://openalex.org/W2537799619","https://openalex.org/W2539213747","https://openalex.org/W2551069776","https://openalex.org/W2564079037","https://openalex.org/W2582416435","https://openalex.org/W2591562181","https://openalex.org/W2602339788","https://openalex.org/W2602439962","https://openalex.org/W2738696838","https://openalex.org/W2742822384","https://openalex.org/W2758731014","https://openalex.org/W2768240280","https://openalex.org/W2771098038","https://openalex.org/W2771334466","https://openalex.org/W2782908004","https://openalex.org/W2783222708","https://openalex.org/W2788391790","https://openalex.org/W2791540588","https://openalex.org/W2793203156","https://openalex.org/W2799653688","https://openalex.org/W2799881328","https://openalex.org/W2800434159","https://openalex.org/W2802308753","https://openalex.org/W2804063886","https://openalex.org/W2807184840","https://openalex.org/W2810473995","https://openalex.org/W2888655585","https://openalex.org/W2889600913","https://openalex.org/W2890887245","https://openalex.org/W2891398053","https://openalex.org/W2901214479","https://openalex.org/W2905278757","https://openalex.org/W2910976973","https://openalex.org/W2911471536","https://openalex.org/W2913500366","https://openalex.org/W2921157022","https://openalex.org/W2940509467","https://openalex.org/W2945365545","https://openalex.org/W2952276154","https://openalex.org/W2952366981","https://openalex.org/W2954970901","https://openalex.org/W2955994124","https://openalex.org/W2969419817","https://openalex.org/W2969514577","https://openalex.org/W2969924257","https://openalex.org/W2970321499","https://openalex.org/W2972345212","https://openalex.org/W2972643014","https://openalex.org/W2982249296","https://openalex.org/W2984291770","https://openalex.org/W2994713430","https://openalex.org/W2999317669","https://openalex.org/W3003424148","https://openalex.org/W3007046486","https://openalex.org/W3007570075","https://openalex.org/W3045007120","https://openalex.org/W3092652421","https://openalex.org/W3112020255"],"related_works":["https://openalex.org/W2804063886","https://openalex.org/W2585951544","https://openalex.org/W4319310830","https://openalex.org/W2807184840","https://openalex.org/W6902086055","https://openalex.org/W2019635124","https://openalex.org/W2023172924","https://openalex.org/W4399296988","https://openalex.org/W2148239117","https://openalex.org/W2783222708"],"abstract_inverted_index":{"Plant":[0],"pathogens":[1,63],"can":[2],"rapidly":[3,73],"overcome":[4],"resistance":[5],"of":[6,36,71,85],"their":[7],"hosts":[8],"by":[9,21],"mutating":[10],"key":[11,65],"pathogenicity":[12],"genes":[13,52,57],"encoding":[14],"for":[15],"effectors.":[16],"Pathogen":[17],"adaptation":[18,95],"is":[19],"fuelled":[20],"extensive":[22],"genetic":[23],"variability":[24],"in":[25,43],"populations":[26],"and":[27,55,83,106,110],"different":[28],"strains":[29],"may":[30],"not":[31],"share":[32],"the":[33,72,81,92],"same":[34],"set":[35],"genes.":[37],"Recently,":[38],"such":[39],"an":[40],"intra-specific":[41],"variation":[42],"gene":[44],"content":[45],"became":[46],"formalized":[47],"as":[48],"pangenomes":[49,87,101],"distinguishing":[50],"core":[51],"(i.e.":[53,58],"shared)":[54],"accessory":[56,75],"lineage":[59],"or":[60],"strain-specific).":[61],"Across":[62],"species,":[64],"effectors":[66],"tend":[67],"to":[68],"be":[69,104],"part":[70],"evolving":[74],"genome.":[76],"Here,":[77],"we":[78],"show":[79],"how":[80,100,107],"construction":[82],"analysis":[84],"pathogen":[86],"provide":[88],"deep":[89],"insights":[90],"into":[91],"dynamic":[93],"host":[94],"process.":[96],"We":[97],"also":[98],"discuss":[99],"should":[102],"ideally":[103],"built":[105],"geography,":[108],"niche":[109],"lifestyle":[111],"likely":[112],"determine":[113],"pangenome":[114],"sizes.":[115]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":26}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2020-06-05T00:00:00"}
