{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T14:36:17Z","timestamp":1787150177953,"version":"build-2736575974"},"reference-count":51,"publisher":"American Chemical Society (ACS)","issue":"32","license":[{"start":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T00:00:00Z","timestamp":1785974400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T00:00:00Z","timestamp":1785974400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T00:00:00Z","timestamp":1785974400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100022960","name":"Guangdong Provincial Special Fund for Modern Agriculture Industry Technology Innovation Teams","doi-asserted-by":"publisher","award":["2024CXTD07"],"award-info":[{"award-number":["2024CXTD07"]}],"id":[{"id":"10.13039\/100022960","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2024YFD1401203-5"],"award-info":[{"award-number":["2024YFD1401203-5"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012453","name":"China Agricultural Research System","doi-asserted-by":"publisher","award":["CARS-10-Sweetpotato"],"award-info":[{"award-number":["CARS-10-Sweetpotato"]}],"id":[{"id":"10.13039\/501100012453","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Bacterial stem and root rot (BSRR), caused by Dickeya dadantii, is a devastating disease affecting sweetpotato [Ipomoea batatas (L.) Lam.] worldwide, yet the pathogen\u2019s population structure and core virulence determinants remain poorly understood. Here, we constructed the first comprehensive pangenome of D. dadantii by integrating complete PacBio HiFi sequencing of a representative strain (E36) with resequencing of 32 Chinese isolates and 23 global strains. Population genomic analysis revealed that geographic isolation and host adaptation drive genetic differentiation, with sweetpotato-associated Chinese strains clustering into two major lineages (Groups I and II). Mining the core genome identified 36 conserved candidate effectors, of which CpxP and Spy were experimentally validated as virulence factors: both triggered a hypersensitive response in Nicotiana benthamiana, and their deletion mutants exhibited attenuated virulence on sweetpotato. This study delineates the population architecture of the BSRR pathogen and uncovers key virulence determinants.<\/jats:p>","DOI":"10.1021\/acs.jafc.6c06279","type":"journal-article","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T05:02:54Z","timestamp":1785992574000},"page":"25075-25088","source":"Crossref","is-referenced-by-count":0,"title":["Pangenome Analysis\nUncovers Two Pathotypes of\n                    <i>Dickeya dadantii<\/i>\n                    , the Causal Agent of Sweetpotato\nStem Rot, and Identifies Virulence-Associated Genes"],"prefix":"10.1021","volume":"74","author":[{"given":"Mengjia","family":"Fan","sequence":"first","affiliation":[{"name":"Crops Research Institute, Guangdong Academy of Agricultural Sciences , , ,","place":["Guangzhou, China, 510640"]},{"name":"Huazhong Agricultural University , , ,","place":["Wuhan, China, 430070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiawei","family":"Ding","sequence":"additional","affiliation":[{"name":"Crops Research Institute, Guangdong Academy of Agricultural Sciences , , ,","place":["Guangzhou, China, 510640"]},{"name":"South China Agricultural University , , , ,","place":["Guangzhou, Guangdong, China, 510640"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianyu","family":"Shi","sequence":"additional","affiliation":[{"name":"Crops Research Institute, Guangdong Academy of Agricultural Sciences , , ,","place":["Guangzhou, China, 510640"]},{"name":"Huazhong Agricultural University , , ,","place":["Wuhan, China, 430070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaowen","family":"Wu","sequence":"additional","affiliation":[{"name":"Guangdong Academy of Agricultural Sciences , , , ,","place":["Guangzhou, Guangdong, China, 510642"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianuan","family":"Zhou","sequence":"additional","affiliation":[{"name":"South China Agricultural University , , , ,","place":["Guangzhou, Guangdong, China, 510640"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongda","family":"Zou","sequence":"additional","affiliation":[{"name":"Crops Research Institute, Guangdong Academy of Agricultural Sciences , , ,","place":["Guangzhou, China, 510640"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhangying","family":"Wang","sequence":"additional","affiliation":[{"name":"Crops Research Institute, Guangdong Academy of Agricultural Sciences , , ,","place":["Guangzhou, China, 510640"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiatao","family":"Xie","sequence":"additional","affiliation":[{"name":"Huazhong Agricultural University , , ,","place":["Wuhan, China, 430070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2107-5808","authenticated-orcid":true,"given":"Lifei","family":"Huang","sequence":"additional","affiliation":[{"name":"Crops Research Institute, Guangdong Academy of Agricultural Sciences , , ,","place":["Guangzhou, China, 510640"]},{"name":"Shanwei Academy of Agricultural Sciences , , ,","place":["Shanwei, Guangdong, China, 516600"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,6]]},"reference":[{"issue":"1","key":"2026081910165782900_cit1","doi-asserted-by":"publisher","first-page":"1082","DOI":"10.1186\/s12870-024-05774-2","article-title":"Comparative analyses of RNA-seq and phytohormone data\nof sweetpotatoes inoculated with Dickeya dadantii causing bacterial stem and root rot of sweetpotato","volume":"24","author":"Xie","year":"2024","journal-title":"BMC Plant Biol."},{"issue":"1","key":"2026081910165782900_cit2","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1146\/annurev-micro-041222-012242","article-title":"Dickeya Diversity and Pathogenic Mechanisms","volume":"78","author":"Zhou","year":"2024","journal-title":"Annu.\nRev. Microbiol."},{"issue":"4","key":"2026081910165782900_cit3","doi-asserted-by":"publisher","first-page":"817","DOI":"10.3390\/microorganisms11040817","article-title":"Biocontrol of Soft Rot Dickeya and Pectobacterium Pathogens by Broad-Spectrum Antagonistic\nBacteria within Paenibacillus polymyxa Complex","volume":"11","author":"Hossain","year":"2023","journal-title":"Microorganisms"},{"issue":"3","key":"2026081910165782900_cit4","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1111\/mpp.12549","article-title":"Transcriptome\nanalysis of the Dickeya dadantii PecS regulon during\nthe early stages of interaction with Arabidopsis thaliana","volume":"19","author":"Pe\u0301dron","year":"2018","journal-title":"Mol. Plant Pathol."},{"key":"2026081910165782900_cit5","doi-asserted-by":"publisher","first-page":"1168480","DOI":"10.3389\/fpls.2023.1168480","article-title":"Insight into biodiversity of the\nrecently rearranged genus Dickeya","volume":"14","author":"Hugouvieux-Cotte-Pattat","year":"2023","journal-title":"Front. Plant Sci."},{"key":"2026081910165782900_cit6","doi-asserted-by":"publisher","first-page":"1806","DOI":"10.1016\/j.csbj.2021.03.019","article-title":"Computational\nprediction\nof secreted proteins in gram-negative bacteria","volume":"19","author":"Hui","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"issue":"1","key":"2026081910165782900_cit7","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1038\/s41564-023-01555-z","article-title":"Leaf microbiome dysbiosis triggered by T2SS-dependent\nenzyme secretion from opportunistic Xanthomonas pathogens","volume":"9","author":"Pfeilmeier","year":"2024","journal-title":"Nat. Microbiol."},{"issue":"2","key":"2026081910165782900_cit8","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved\nde novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"Cheng","year":"2021","journal-title":"Nat. Methods"},{"key":"2026081910165782900_cit9","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition\nand translation\ninitiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinf."},{"issue":"1","key":"2026081910165782900_cit10","doi-asserted-by":"publisher","first-page":"4.10.1","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker\nto identify repetitive elements in genomic sequences","volume":"25","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr. Protoc. 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Biol."},{"issue":"1","key":"2026081910165782900_cit23","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic\northology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"issue":"D1","key":"2026081910165782900_cit24","doi-asserted-by":"publisher","first-page":"D427","DOI":"10.1093\/nar\/gky995","article-title":"The Pfam protein families database in 2019","volume":"47","author":"El-Gebali","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2026081910165782900_cit25","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1007\/978-1-59745-251-9_3","article-title":"Multiple alignment\nof DNA sequences\nwith MAFFT","volume":"537","author":"Katoh","year":"2009","journal-title":"Methods Mol. Biol."},{"issue":"4","key":"2026081910165782900_cit26","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1080\/10635150701472164","article-title":"Improvement\nof phylogenies after removing divergent\nand ambiguously aligned blocks from protein sequence alignments","volume":"56","author":"Talavera","year":"2007","journal-title":"Syst. Biol."},{"issue":"1","key":"2026081910165782900_cit27","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast\nand effective stochastic algorithm for estimating maximum-likelihood\nphylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"issue":"3","key":"2026081910165782900_cit28","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting\ntransmembrane protein topology with a hidden Markov model: application\nto complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"issue":"5","key":"2026081910165782900_cit29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0020269","article-title":"lpxC and yafS\nare the most suitable internal controls to normalize real time RT-qPCR\nexpression in the phytopathogenic bacteria Dickeya dadantii","volume":"6","author":"Hommais","year":"2011","journal-title":"PLoS One"},{"issue":"1","key":"2026081910165782900_cit30","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/s43897-024-00086-3","article-title":"Characterization of two SGNH family cell death-inducing\nproteins\nfrom the horticulturally important fungal pathogen Botrytis cinerea\nbased on the optimized prokaryotic expression system","volume":"4","author":"Zhang","year":"2024","journal-title":"Mol. Hortic."},{"issue":"9","key":"2026081910165782900_cit31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0137466","article-title":"Cloning Should Be Simple: Escherichia coli DH5\u03b1-Mediated Assembly of\nMultiple DNA Fragments with Short End Homologies","volume":"10","author":"Kostylev","year":"2015","journal-title":"PLoS One"},{"issue":"3","key":"2026081910165782900_cit32","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1007\/BF00436188","article-title":"High frequency\nmobilization of gram-negative bacterial replicons by the in vitro\nconstructed Tn5-Mob transposon","volume":"196","author":"Simon","year":"1984","journal-title":"Mol. Gen. Genet."},{"issue":"9","key":"2026081910165782900_cit33","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information\naesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"issue":"1","key":"2026081910165782900_cit34","doi-asserted-by":"publisher","first-page":"veac031","DOI":"10.1093\/ve\/veac031","article-title":"ANI analysis of poxvirus genomes\nreveals its potential application to viral species rank demarcation","volume":"8","author":"Deng","year":"2022","journal-title":"Virus Evol."},{"issue":"12","key":"2026081910165782900_cit35","doi-asserted-by":"publisher","first-page":"1503","DOI":"10.1094\/PDIS-06-10-0417","article-title":"First Report of Bacterial Stem and Root Rot of Sweetpotato\nCaused by a Dickeya sp. (Erwinia chrysanthemi) in China","volume":"94","author":"Huang","year":"2010","journal-title":"Plant Dis."},{"issue":"Pt 10","key":"2026081910165782900_cit36","doi-asserted-by":"publisher","first-page":"2388","DOI":"10.1099\/ijs.0.009258-0","article-title":"Dickeya species relatedness and clade\nstructure determined by comparison of recA sequences","volume":"59","author":"Parkinson","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"issue":"6","key":"2026081910165782900_cit37","doi-asserted-by":"publisher","first-page":"1227","DOI":"10.13802\/j.cnki.zwbhxb.2018.2017112","article-title":"Pathogenic differentiation and genetic\ndiversity of Dickeya dadantii causing bacterial stem\nand root rot of\nsweetpotato","volume":"45","author":"Huang","year":"2018","journal-title":"J. Plant Prot."},{"issue":"8","key":"2026081910165782900_cit38","doi-asserted-by":"publisher","first-page":"643","DOI":"10.3390\/biology15080643","article-title":"Genome-Wide\nAssociation\nStudy and Candidate Gene Identification for Resistance to Bacterial\nStem and Root Rot in Sweetpotato","volume":"15","author":"Lin","year":"2026","journal-title":"Biology"},{"issue":"12","key":"2026081910165782900_cit39","doi-asserted-by":"publisher","first-page":"3946","DOI":"10.1094\/PDIS-03-21-0587-RE","article-title":"Pangenomic Analysis\nof Dickeya dianthicola Strains Related to the Outbreak\nof Blackleg and Soft Rot of Potato in the United States","volume":"105","author":"Ge","year":"2021","journal-title":"Plant Dis."},{"issue":"2","key":"2026081910165782900_cit40","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02072-21","article-title":"Pan-Genome\nAnalysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic\nDiversity; Pathogenicity; and Biotechnological Properties of the Species","volume":"10","author":"Yin","year":"2022","journal-title":"Microbiol. Spectrum."},{"issue":"7","key":"2026081910165782900_cit41","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.3390\/agronomy14071342","article-title":"High-Quality Complete\nGenome Resource for Dickeya dadantii Type Strain\nDSM 18020 via PacBio Sequencing","volume":"14","author":"Cheng","year":"2024","journal-title":"Agronomy"},{"key":"2026081910165782900_cit42","doi-asserted-by":"publisher","first-page":"822829","DOI":"10.3389\/fpls.2022.822829","article-title":"Genomic Comparisons\nand Phenotypic\nDiversity of Dickeya zeae Strains Causing Bacterial\nSoft Rot of Banana in China","volume":"13","author":"Zhang","year":"2022","journal-title":"Front. Plant Sci."},{"issue":"8","key":"2026081910165782900_cit43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0002973","article-title":"Type III secretion\nsystem genes of Dickeya dadantii 3937 are induced by plant phenolic acids","volume":"3","author":"Yang","year":"2008","journal-title":"PLoS One"},{"key":"2026081910165782900_cit44","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1016\/j.csbj.2023.09.043","article-title":"Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9; pan-genomic and genetic\nbasis of biocontrol mechanism","volume":"21","author":"Asif","year":"2023","journal-title":"Comput. Struct.\nBiotechnol. J."},{"issue":"1","key":"2026081910165782900_cit45","doi-asserted-by":"publisher","first-page":"101446","DOI":"10.1016\/j.jbc.2021.101446","article-title":"Carbon catabolite repression in pectin digestion by the phytopathogen Dickeya dadantii","volume":"298","author":"Shiny","year":"2022","journal-title":"J. Biol. Chem."},{"issue":"2","key":"2026081910165782900_cit46","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01805-21","article-title":"Quorum-Sensing Master\nRegulator VfmE Is a c-di-GMP\nEffector That Controls Pectate Lyase Production in the Phytopathogen Dickeya dadantii","volume":"10","author":"Banerjee","year":"2022","journal-title":"Microbiol. Spectrum."},{"key":"2026081910165782900_cit47","doi-asserted-by":"publisher","first-page":"1360524","DOI":"10.3389\/fmicb.2024.1360524","article-title":"Genome sequencing\nand comparative genome analysis of Rhizoctonia solani AG-3","volume":"15","author":"Xu","year":"2024","journal-title":"Front. Microbiol."},{"issue":"1","key":"2026081910165782900_cit48","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1186\/s13568-020-01099-z","article-title":"Knocking out\nAnalysis\nof the CpxP gene using Crispr\/Cas9 in Escherichia coli MG1655","volume":"10","author":"He","year":"2020","journal-title":"AMB Express"},{"issue":"9","key":"2026081910165782900_cit49","doi-asserted-by":"publisher","first-page":"2149","DOI":"10.1128\/JB.01296-10","article-title":"Structure\nof the periplasmic stress\nresponse protein CpxP","volume":"193","author":"Thede","year":"2011","journal-title":"J. Bacteriol."},{"issue":"9","key":"2026081910165782900_cit50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0107383","article-title":"Dynamic interaction\nbetween the CpxA sensor kinase and the periplasmic accessory protein\nCpxP mediates signal recognition in E. coli","volume":"9","author":"Tschauner","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"2026081910165782900_cit51","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1038\/s41467-021-21120-8","article-title":"Mechanism of\nthe small ATP-independent\nchaperone Spy is substrate specific","volume":"12","author":"Mitra","year":"2021","journal-title":"Nat. Commun."}],"container-title":["Journal of Agricultural\nand Food Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jafc.6c06279","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jafcau\/article-pdf\/74\/32\/25075\/66427688\/acs.jafc.6c06279.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jafcau\/article-pdf\/74\/32\/25075\/66427688\/acs.jafc.6c06279.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T14:22:41Z","timestamp":1787149361000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jafcau\/article\/74\/32\/25075\/5247202\/Pangenome-Analysis-Uncovers-Two-Pathotypes-of"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,6]]},"references-count":51,"journal-issue":{"issue":"32","published-online":{"date-parts":[[2026,8,6]]},"published-print":{"date-parts":[[2026,8,19]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jafc.6c06279","relation":{},"ISSN":["0021-8561","1520-5118"],"issn-type":[{"value":"0021-8561","type":"print"},{"value":"1520-5118","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,6]]}}}