Whole-genome sequence of Xanthomonas arboricola  pv. pruni strain 9-4 causing peach bacterial spot in China

Whole-genome sequence of Xanthomonas arboricola pv. pruni strain 9-4 causing peach bacterial spot in China | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Data Note Whole-genome sequence of Xanthomonas arboricola pv. pruni strain 9-4 causing peach bacterial spot in China Jiayu Yuan, Chun Yan, Junnan Wang, Zhaolin Ji, Lina Yang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7149576/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 29 Oct, 2025 Read the published version in BMC Genomic Data → Version 1 posted 10 You are reading this latest preprint version Abstract Objective: Peach bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), poses a significant threat to the global peach industry. Studies have indicated that 41 Xap strains isolated from various peach cultivars in China exhibit moderate genetic differentiation, clear specificity to peach cultivars, and limited geographical differentiation. The genomic information of 36 Xap strains isolated from different areas has been deposited to the NCBI genome database; However, complete genome sequences for Xap strains identified in China remain lacking. In this study, the whole genome of the Xap 9-4 strain, isolated from diseased peach leaves in China, was assembled and annotated. Data description: The genomic data of the Xap 9-4 strain were sequenced using the Illumina and PacBio platforms. The genome of Xap 9-4 consisted of a 5,174,371 bp circular chromosome and a 41,329 bp circular plasmid, encoding 4,660 protein-coding genes, 201 ncRNAs, 643 repeat regions and 7 prophages. Approximately 94.82% of the proteins were annotated. These findings will expand the genomic resources for Xap and provide a foundation for further studies on genetic diversity and pathogen-host interaction mechanisms. Xanthomonas arboricola pv. pruni Genome assembly Genome annotation Peach Bacterial spot Objective Peach ( Prunus persica (L.) Batsch) is an important economically cultivated fruit trees and is popular to consumers due to its delicious flavor and high nutritional value[ 1 ]. Peach bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is one of the most serious bacterial diseases affecting peach trees worldwide and lead to devastating losses of the peach industry[ 2 , 3 ]. It not only causes bacterial spot on peach leaves and fruits, but also induces stem canker[ 3 ]. The disease was first described in North America in 1903, and further observed in Europe, Africa, Oceanian and Asia[ 4 ]. Additionally, Xap could also infect the most stone fruits (nectarine, plum, apricot, and cherry), and almond[ 5 ]. In the past ten years, bacterial spot has emerged as an epidemic disease in major peach-producing areas of China. Studies have shown that 41 Xap strains isolated from various peach cultivars in China display moderate genetic differentiation, along with distinct host cultivar specificity but weak geographical differentiation [ 6 ]. The whole genome sequences of 36 Xap strains isolated from different areas have been deposited in the NCBI Genome database[ 7 , 8 ]. However, the Xap strains identified in China still lack complete genome sequences. To expand the genomic resources for further exploration of genetic diversity and pathogen-host interaction mechanism, we sequenced the pathogenic Xap strain 9 − 4, which was isolated from diseased peach leaves in China. Data description The Xap 9 − 4 strain was originally isolated from peach leaves within typical bacterial spot symptoms in Wafangdian city, Liaoning province, China (39.627114°N, 121.979603°E) in 2015. A single colony of the Xap 9 − 4 strain was grown overnight in nutrient broth (NB) media using a shaker at 28℃ and 200 rpm. Genomic DNA was extracted using the FastPure Bacterial DNA Isolation Mini Kit (DC103, Vazyme, Nanjing, China). The concentration of genomic DNA was measured using a Qubit fluorometer (Invitrogen), and the integrity and purity were assessed by 1% agarose gel electrophoresis. The Xap 9 − 4 genome was sequenced using the Illumina HiSeq 4000 (second-generation sequencing) and the PacBio RS II (third-generation sequencing) platform at the Beijing Genomics Institute (BGI, Shenzhen, China). Draft genomic unitigs, which represent unambiguous groups of fragments, were assembled using the Celera Assembler (v8.3) based on a high-quality corrected circular consensus sequence subreads set. To improve the accuracy of the genome sequences, GATK (v1.6-13) was used to make single-base corrections. There were two contigs, and the complete genome of the Xap 9 − 4 strain was 5,174,371 bp with a GC content of 65.37%, consisting of one chromosome (5,133,042 bp in length with a GC content of 65.39%) and one plasmid (41,329 bp in length within a GC content of 62.73%) (Data file 1, Table 1 ) [ 9 ]. As shown in Data file 2, the genomic assembly sequences were submitted to the NCBI GenBank Database with accession number CP182134 and CP182135 under Bioproject number PRJNA1148038, representing the chromosome and plasmid of the Xap 9 − 4 strain [ 10 ]. Gene prediction was conducted on the 9 − 4 genome assembly using Glimmer (v3.02) with Hidden Markov models[ 11 ]. tRNA, rRNA, and sRNAs were identified using tRNAscan-SE (v1.3.1)[ 12 ], RNAmmer (v1.2)[ 13 ], and Rfam database (v9.1)[ 14 ]. Tandem repeats annotation was performed using the Tandem Repeat Finder (v4.04), and minisatellite DNA and microsatellite DNA identified based on the number and length of repeat units. Prophage regions were predicted using the PHAST (v2013.03.20)[ 15 ]. The 9 − 4 genome contains 4,660 protein-coding genes, 201 ncRNAs, 643 repeat regions, 7 prophages (Data file 1, Table 1 ) [ 9 ]. Circular representations of the genome and plasmid were presented in Data file 3[ 9 ]. Seven databases, which are KEGG, COG, NR, Swiss-Prot, GO, TrEMBL, and EggNOG, were used for general function annotation. Four databases were employed for pathogenicity and drug resistance analysis. Virulence factors and resistance gene were identified based on the core dataset in VFDB and ARDB databases; two additional databases used were PHI and CAZy. Type III secretion system effector proteins were detected using EffectiveT3. These results are presented in Data file 1 and Data file 3. Protein annotations, CDS sequences, amino acids sequences, and predicted Type III effectors of the Xap 9 − 4 strain were provided in Supplementary Data file 4–7 [ 9 ]. In conclusion, this study presented the complete genomic information of the Xap 9 − 4 strain causing peach bacterial spot on leaves in China. The availability of these data provides a solid foundation for investigating the genetic diversity and pathogen-host interaction mechanisms. Table 1 Overview of data files/data sets Label Name of data file/data set File types (File extension) Data repository and identifier (DOI or accession number) Data file 1 Genomic analysis, BGISEQ statistics, PacBio Reads statistics, k-mer statistics, genomic assembly statistics, genomic feature, ncRNA statistics, repeat statistics, prophage statistics and Genomic annotation statistics of Xanthomonas arboricola pv. pruni strain 9 − 4 Word file (.docx) https://doi.org/10.6084/m9.figshare.29573585.v1 [ 9 ] Data file 2 Genome assembly of Xanthomonas arboricola pv. pruni strain 9 − 4 Fasta file (.fasta) http://www.ncbi.nlm.nih.gov/datasets/genome/GCF_048013395.1/ [ 10 ] Data file 3 Circular representation of genome and plasmid, gene length distribution, COG, GO and KEGG annotation of Xanthomonas arboricola pv. pruni strain 9 − 4 Word file (.docx) https://doi.org/10.6084/m9.figshare.29573585.v1 [ 9 ] Data file 4 Protein annotation of Xanthomonas arboricola pv. pruni strain 9 − 4 Excel file (.xlsx) https://doi.org/10.6084/m9.figshare.29573585.v1 [ 9 ] Data file 5 CDS sequence of Xanthomonas arboricola pv. pruni strain 9 − 4 Fasta file (.fasta) https://doi.org/10.6084/m9.figshare.29573585.v1 [ 9 ] Data file 6 Amino acids sequence of Xanthomonas arboricola pv. pruni strain 9 − 4 Fasta file (.fasta) https://doi.org/10.6084/m9.figshare.29573585.v1 [ 9 ] Data file 7 Predicted type III effectors in Xanthomonas arboricola pv. pruni strain 9 − 4 Excel file (.xlsx) https://doi.org/10.6084/m9.figshare.29573585.v1 [ 9 ] Limitations This Data Note presents high-quality genomic information of the Xap 9 − 4 strain based on data from both PacBio and Illumina platform. However, the genome assembly still consists of two contigs, indicating the presence of unresolved genomic regions. Furthermore, no comparative genomic analysis has been conducted across different Xap strains isolated from various hosts or geographic regions. Abbreviations Xap Xanthomonas arboricola pv. pruni DNA Deoxyribonucleic acid NB Nutrient broth Bp Base pair KEGG Kyoto Encyclopedia of Genes and Genomes COG Clusters of Orthologous Groups NR NonRedundant Protein Database databases GO Gene Ontology PHAST PHAge Search Tool VFDB Virulence Factors of Pathogenic Bacteria ARDB Antibiotic Resistance Genes Database PHI Pathogen Host Interactions CAZy Carbohydrate-Active enZYmes Database Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare no competing interests. Funding The research was financially supported by the China Agriculture Research System of MOF and MARA (Grant No. CARS-30-3-02) and the National Natural Science Foundation of China (32202237). Author Contribution JYY, CY, and JNW: strain isolated, purified, cultivation and DNA extraction. LNY：designed the experiment, performed the genome analysis and prepared the manuscript. ZLJ: designed the experiment and supervised the project. All authors read and approved the final manuscript. Acknowledgement The authors appreciate the Beijing Genomics institution (Wuhan, China) for providing high-quality sequencing. Availability of data and materials The data described in this Data note can be freely and openly accessed on Figshare ( https://figshare.com/ ) for Supplementary data file 1, 3–7 [ 9 ]. Data file 2 is available on the NCBI GenBank under the Bioproject number PRJNA1148038 [ 10 ]. Please see table 1 and references [ 9 – 10 ] for details and links to the data. References Xin R, Liu X, Wei C, Yang C, Liu H, Cao X, Wu D, Zhang B, Chen K. E-Nose and GC-MS reveal a difference in the volatile profiles of white- and red-fleshed peach fruit. Sens (Basel) 2018, 18(3). Suesada Y, Yamada M, Sawamura Y, Adachi E, Yaegaki H, Yamaguchi M, Yamamoto T. Inheritance of susceptibility to bacterial spot (Xanthomonas arboricola pv. pruni) in peach offspring populations derived from Brazilian and Japanese cultivars/selections. Breed Sci. 2019;69(1):11–8. Cox BM, Wang H, Schnabel G. Copper tolerance in Xanthomonas arboricola pv. pruni in south Carolina peach orchards. Plant Dis. 2022;106(6):1626–31. Boudon S, Manceau C, Nottéghem JL. Structure and origin of Xanthomonas arboricola pv. pruni populations causing bacterial spot of stone fruit trees in western Europe. Phytopathology. 2005;95(9):1081–8. Garita-Cambronero J, Palacio-Bielsa A, Cubero J. Xanthomonas arboricola pv. pruni, causal agent of bacterial spot of stone fruits and almond: its genomic and phenotypic characteristics in the X. arboricola species context. Mol Plant Pathol. 2018;19(9):2053–65. Luo M, Meng F-Z, Tan Q, Zhou Y, Chaisiri C, Fan F, Yin W-X, Luo C-X. Identification, genetic diversity, and chemical control of Xanthomonas arboricola pv. pruni in China. Plant Dis. 2022;106(9):2415–23. Garita-Cambronero J, Sena-Vélez M, Palacio-Bielsa A, Cubero J. Draft genome sequence of Xanthomonas arboricola pv. pruni strain Xap33, causal agent of bacterial spot disease on almond. Genome Announcements 2014, 2(3). Dimaria G, Mosca A, Russo M, Cubero J, Pothier JF, Koebnik R, Catara V. Draft genome sequence of Xanthomonas arboricola pv. pruni PVCT 262.1 isolated from Prunus dulcis in italy. Microbiol Resour Announc. 2024;13(7):e0027324. Yang L. Whole-genome sequence information of Xanthomonas arboricola pv. pruni strain 9 – 4 causing peach bacterial spot in China. figshare. Dataset. https://figshare.com/articles/dataset/_/29573585 (2025). National Center for Biotechnology Information. Assembly. http://www.ncbi.nlm.nih.gov/datasets/genome/GCF_048013395.1/ (2025). Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6):673–9. Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 2021;49(16):9077–96. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100–8. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res. 2009;37(Database issue):D136–140. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011, 39(Web Server issue):W347–352. Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 29 Oct, 2025 Read the published version in BMC Genomic Data → Version 1 posted Editorial decision: Revision requested 05 Sep, 2025 Reviews received at journal 13 Aug, 2025 Reviews received at journal 09 Aug, 2025 Reviewers agreed at journal 06 Aug, 2025 Reviewers agreed at journal 05 Aug, 2025 Reviewers agreed at journal 05 Aug, 2025 Reviewers invited by journal 05 Aug, 2025 Editor assigned by journal 28 Jul, 2025 Submission checks completed at journal 28 Jul, 2025 First submitted to journal 17 Jul, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7149576","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Data Note","associatedPublications":[],"authors":[{"id":496473580,"identity":"6a57d12d-8fe5-4db0-99c0-1a2047999420","order_by":0,"name":"Jiayu Yuan","email":"","orcid":"","institution":"Yangzhou University","correspondingAuthor":false,"prefix":"","firstName":"Jiayu","middleName":"","lastName":"Yuan","suffix":""},{"id":496473581,"identity":"05ec00ec-889a-41d5-bdee-157ec7894cd3","order_by":1,"name":"Chun Yan","email":"","orcid":"","institution":"Yangzhou University","correspondingAuthor":false,"prefix":"","firstName":"Chun","middleName":"","lastName":"Yan","suffix":""},{"id":496473582,"identity":"5bc2f5e6-74cd-4fc1-a6fd-79a92b9d9366","order_by":2,"name":"Junnan Wang","email":"","orcid":"","institution":"Yangzhou University","correspondingAuthor":false,"prefix":"","firstName":"Junnan","middleName":"","lastName":"Wang","suffix":""},{"id":496473583,"identity":"90a7972f-5926-4c25-a78f-893b7a84dc00","order_by":3,"name":"Zhaolin Ji","email":"","orcid":"","institution":"Yangzhou University","correspondingAuthor":false,"prefix":"","firstName":"Zhaolin","middleName":"","lastName":"Ji","suffix":""},{"id":496473584,"identity":"5db61e55-34ec-4e99-bb39-476360269774","order_by":4,"name":"Lina Yang","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA6ElEQVRIiWNgGAWjYBACPmYog429sfHBBwMbO4Ja2GBa+HkOHzacUZCWTFgLjCE5Iy1NmufDIcYGglrYeQ9+5qm5Y7fhRo6ZtI3BAWYG9sNHN+B3GF+yNM+xZ8kbzrwxts4xuMPHwJOWdgO/Fh4DaR62w8kGx3MMb+cYPGNmkOAxI6TF+DfPP6CWAzkG0hYGhxkbiNBiJs3bdthOsiMtSZqBWC2Wc/sOJ4ADuccgLZmNkF/4+c8Y33jz7bA9OCp//LGx42c/fAyvFhBg4mFgSGyA20tIOQgw/mBgsCdG4SgYBaNgFIxQAABOOUeWUVvxwQAAAABJRU5ErkJggg==","orcid":"","institution":"Yangzhou University","correspondingAuthor":true,"prefix":"","firstName":"Lina","middleName":"","lastName":"Yang","suffix":""}],"badges":[],"createdAt":"2025-07-17 13:38:11","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7149576/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7149576/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12863-025-01377-4","type":"published","date":"2025-10-29T15:57:16+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":95039918,"identity":"5fc6a740-93a1-4b10-95ec-aab752c8e172","added_by":"auto","created_at":"2025-11-03 16:05:43","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":463328,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7149576/v1/ea7268b5-1cc2-4ce9-83a1-f54785fbf2ef.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Whole-genome sequence of Xanthomonas arboricola pv. pruni strain 9-4 causing peach bacterial spot in China","fulltext":[{"header":"Objective","content":"\u003cp\u003ePeach (\u003cem\u003ePrunus persica\u003c/em\u003e (L.) Batsch) is an important economically cultivated fruit trees and is popular to consumers due to its delicious flavor and high nutritional value[\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. Peach bacterial spot, caused by \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e (Xap), is one of the most serious bacterial diseases affecting peach trees worldwide and lead to devastating losses of the peach industry[\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. It not only causes bacterial spot on peach leaves and fruits, but also induces stem canker[\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. The disease was first described in North America in 1903, and further observed in Europe, Africa, Oceanian and Asia[\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Additionally, Xap could also infect the most stone fruits (nectarine, plum, apricot, and cherry), and almond[\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eIn the past ten years, bacterial spot has emerged as an epidemic disease in major peach-producing areas of China. Studies have shown that 41 Xap strains isolated from various peach cultivars in China display moderate genetic differentiation, along with distinct host cultivar specificity but weak geographical differentiation [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. The whole genome sequences of 36 Xap strains isolated from different areas have been deposited in the NCBI Genome database[\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. However, the Xap strains identified in China still lack complete genome sequences. To expand the genomic resources for further exploration of genetic diversity and pathogen-host interaction mechanism, we sequenced the pathogenic Xap strain 9 − 4, which was isolated from diseased peach leaves in China.\u003c/p\u003e"},{"header":"Data description","content":"\u003cp\u003eThe Xap 9 − 4 strain was originally isolated from peach leaves within typical bacterial spot symptoms in Wafangdian city, Liaoning province, China (39.627114°N, 121.979603°E) in 2015. A single colony of the Xap 9 − 4 strain was grown overnight in nutrient broth (NB) media using a shaker at 28℃ and 200 rpm. Genomic DNA was extracted using the FastPure Bacterial DNA Isolation Mini Kit (DC103, Vazyme, Nanjing, China). The concentration of genomic DNA was measured using a Qubit fluorometer (Invitrogen), and the integrity and purity were assessed by 1% agarose gel electrophoresis.\u003c/p\u003e\u003cp\u003eThe Xap 9 − 4 genome was sequenced using the Illumina HiSeq 4000 (second-generation sequencing) and the PacBio RS II (third-generation sequencing) platform at the Beijing Genomics Institute (BGI, Shenzhen, China). Draft genomic unitigs, which represent unambiguous groups of fragments, were assembled using the Celera Assembler (v8.3) based on a high-quality corrected circular consensus sequence subreads set. To improve the accuracy of the genome sequences, GATK (v1.6-13) was used to make single-base corrections. There were two contigs, and the complete genome of the Xap 9 − 4 strain was 5,174,371 bp with a GC content of 65.37%, consisting of one chromosome (5,133,042 bp in length with a GC content of 65.39%) and one plasmid (41,329 bp in length within a GC content of 62.73%) (Data file 1, Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e) [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. As shown in Data file 2, the genomic assembly sequences were submitted to the NCBI GenBank Database with accession number CP182134 and CP182135 under Bioproject number PRJNA1148038, representing the chromosome and plasmid of the Xap 9 − 4 strain [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eGene prediction was conducted on the 9 − 4 genome assembly using Glimmer (v3.02) with Hidden Markov models[\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. tRNA, rRNA, and sRNAs were identified using tRNAscan-SE (v1.3.1)[\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e], RNAmmer (v1.2)[\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e], and Rfam database (v9.1)[\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. Tandem repeats annotation was performed using the Tandem Repeat Finder (v4.04), and minisatellite DNA and microsatellite DNA identified based on the number and length of repeat units. Prophage regions were predicted using the PHAST (v2013.03.20)[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. The 9 − 4 genome contains 4,660 protein-coding genes, 201 ncRNAs, 643 repeat regions, 7 prophages (Data file 1, Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e) [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. Circular representations of the genome and plasmid were presented in Data file 3[\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eSeven databases, which are KEGG, COG, NR, Swiss-Prot, GO, TrEMBL, and EggNOG, were used for general function annotation. Four databases were employed for pathogenicity and drug resistance analysis. Virulence factors and resistance gene were identified based on the core dataset in VFDB and ARDB databases; two additional databases used were PHI and CAZy. Type III secretion system effector proteins were detected using EffectiveT3. These results are presented in Data file 1 and Data file 3. Protein annotations, CDS sequences, amino acids sequences, and predicted Type III effectors of the Xap 9 − 4 strain were provided in Supplementary Data file 4–7 [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eIn conclusion, this study presented the complete genomic information of the Xap 9 − 4 strain causing peach bacterial spot on leaves in China. The availability of these data provides a solid foundation for investigating the genetic diversity and pathogen-host interaction mechanisms.\u003c/p\u003e\u003cdiv class=\"gridtable\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eOverview of data files/data sets\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"4\"\u003e\u003c/colgroup\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eLabel\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eName of data file/data set\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003eFile types (File extension)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eData repository and identifier (DOI or accession number)\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eData file 1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eGenomic analysis, BGISEQ statistics, PacBio Reads statistics, k-mer statistics, genomic assembly statistics, genomic feature, ncRNA statistics, repeat statistics, prophage statistics and Genomic annotation statistics of \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e strain 9 − 4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eWord file (.docx)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.29573585.v1\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.29573585.v1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eData file 2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eGenome assembly of \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e strain 9 − 4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eFasta file (.fasta)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://www.ncbi.nlm.nih.gov/datasets/genome/GCF_048013395.1/\u003c/span\u003e\u003cspan address=\"http://www.ncbi.nlm.nih.gov/datasets/genome/GCF_048013395.1/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eData file 3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eCircular representation of genome and plasmid, gene length distribution, COG, GO and KEGG annotation of \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e strain 9 − 4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eWord file (.docx)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.29573585.v1\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.29573585.v1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eData file 4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eProtein annotation of \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e strain 9 − 4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eExcel file (.xlsx)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.29573585.v1\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.29573585.v1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eData file 5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eCDS sequence of \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e strain 9 − 4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eFasta file (.fasta)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.29573585.v1\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.29573585.v1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eData file 6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eAmino acids sequence of \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e strain 9 − 4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eFasta file (.fasta)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.29573585.v1\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.29573585.v1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eData file 7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ePredicted type III effectors in \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e strain 9 − 4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eExcel file (.xlsx)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.29573585.v1\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.29573585.v1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/table\u003e\u003c/div\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003cb\u003eLimitations\u003c/b\u003e\u003c/p\u003e\u003cp\u003eThis Data Note presents high-quality genomic information of the Xap 9 − 4 strain based on data from both PacBio and Illumina platform. However, the genome assembly still consists of two contigs, indicating the presence of unresolved genomic regions. Furthermore, no comparative genomic analysis has been conducted across different Xap strains isolated from various hosts or geographic regions.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eXap \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e\u003c/p\u003e\u003cp\u003eDNA Deoxyribonucleic acid\u003c/p\u003e\u003cp\u003eNB Nutrient broth\u003c/p\u003e\u003cp\u003eBp Base pair\u003c/p\u003e\u003cp\u003eKEGG Kyoto Encyclopedia of Genes and Genomes\u003c/p\u003e\u003cp\u003eCOG Clusters of Orthologous Groups\u003c/p\u003e\u003cp\u003eNR NonRedundant Protein Database databases\u003c/p\u003e\u003cp\u003eGO Gene Ontology\u003c/p\u003e\u003cp\u003ePHAST PHAge Search Tool\u003c/p\u003e\u003cp\u003eVFDB Virulence Factors of Pathogenic Bacteria\u003c/p\u003e\u003cp\u003eARDB Antibiotic Resistance Genes Database\u003c/p\u003e\u003cp\u003ePHI Pathogen Host Interactions\u003c/p\u003e\u003cp\u003eCAZy Carbohydrate-Active enZYmes Database\u003c/p\u003e\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003cp\u003eNot applicable.\u003c/p\u003e\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003cp\u003eNot applicable.\u003c/p\u003e\u003c/p\u003e\u003cp\u003e\u003ch2\u003eCompeting interests\u003c/h2\u003e\u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e\u003c/p\u003e\u003ch2\u003eFunding\u003c/h2\u003e\u003cp\u003eThe research was financially supported by the China Agriculture Research System of MOF and MARA (Grant No. CARS-30-3-02) and the National Natural Science Foundation of China (32202237).\u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eJYY, CY, and JNW: strain isolated, purified, cultivation and DNA extraction. LNY：designed the experiment, performed the genome analysis and prepared the manuscript. ZLJ: designed the experiment and supervised the project. All authors read and approved the final manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eThe authors appreciate the Beijing Genomics institution (Wuhan, China) for providing high-quality sequencing.\u003c/p\u003e\u003ch2\u003eAvailability of data and materials\u003c/h2\u003e\u003cp\u003eThe data described in this Data note can be freely and openly accessed on Figshare (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://figshare.com/\u003c/span\u003e\u003cspan address=\"https://figshare.com/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) for Supplementary data file 1, 3\u0026ndash;7 [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. Data file 2 is available on the NCBI GenBank under the Bioproject number PRJNA1148038 [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. Please see table 1 and references [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e] for details and links to the data.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eXin R, Liu X, Wei C, Yang C, Liu H, Cao X, Wu D, Zhang B, Chen K. E-Nose and GC-MS reveal a difference in the volatile profiles of white- and red-fleshed peach fruit. Sens (Basel) 2018, 18(3).\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSuesada Y, Yamada M, Sawamura Y, Adachi E, Yaegaki H, Yamaguchi M, Yamamoto T. Inheritance of susceptibility to bacterial spot (Xanthomonas arboricola pv. pruni) in peach offspring populations derived from Brazilian and Japanese cultivars/selections. Breed Sci. 2019;69(1):11\u0026ndash;8.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eCox BM, Wang H, Schnabel G. Copper tolerance in Xanthomonas arboricola pv. pruni in south Carolina peach orchards. Plant Dis. 2022;106(6):1626\u0026ndash;31.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eBoudon S, Manceau C, Nott\u0026eacute;ghem JL. Structure and origin of Xanthomonas arboricola pv. pruni populations causing bacterial spot of stone fruit trees in western Europe. Phytopathology. 2005;95(9):1081\u0026ndash;8.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eGarita-Cambronero J, Palacio-Bielsa A, Cubero J. Xanthomonas arboricola pv. pruni, causal agent of bacterial spot of stone fruits and almond: its genomic and phenotypic characteristics in the X. arboricola species context. Mol Plant Pathol. 2018;19(9):2053\u0026ndash;65.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLuo M, Meng F-Z, Tan Q, Zhou Y, Chaisiri C, Fan F, Yin W-X, Luo C-X. Identification, genetic diversity, and chemical control of Xanthomonas arboricola pv. pruni in China. Plant Dis. 2022;106(9):2415\u0026ndash;23.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eGarita-Cambronero J, Sena-V\u0026eacute;lez M, Palacio-Bielsa A, Cubero J. Draft genome sequence of Xanthomonas arboricola pv. pruni strain Xap33, causal agent of bacterial spot disease on almond. Genome Announcements 2014, 2(3).\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eDimaria G, Mosca A, Russo M, Cubero J, Pothier JF, Koebnik R, Catara V. Draft genome sequence of Xanthomonas arboricola pv. pruni PVCT 262.1 isolated from Prunus dulcis in italy. Microbiol Resour Announc. 2024;13(7):e0027324.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eYang L. Whole-genome sequence information of Xanthomonas arboricola pv. pruni strain 9\u0026thinsp;\u0026ndash;\u0026thinsp;4 causing peach bacterial spot in China. figshare. Dataset. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://figshare.com/articles/dataset/_/29573585\u003c/span\u003e\u003cspan address=\"https://figshare.com/articles/dataset/_/29573585\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e(2025).\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eNational Center for Biotechnology Information. Assembly. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://www.ncbi.nlm.nih.gov/datasets/genome/GCF_048013395.1/\u003c/span\u003e\u003cspan address=\"http://www.ncbi.nlm.nih.gov/datasets/genome/GCF_048013395.1/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e (2025).\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eDelcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6):673\u0026ndash;9.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eChan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 2021;49(16):9077\u0026ndash;96.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLagesen K, Hallin P, R\u0026oslash;dland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100\u0026ndash;8.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eGardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res. 2009;37(Database issue):D136\u0026ndash;140.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011, 39(Web Server issue):W347\u0026ndash;352.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomic-data","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gtic","sideBox":"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gtic/default.aspx","title":"BMC Genomic Data","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Xanthomonas arboricola pv. pruni, Genome assembly, Genome annotation, Peach, Bacterial spot","lastPublishedDoi":"10.21203/rs.3.rs-7149576/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7149576/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eObjective:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePeach bacterial spot, caused by \u003cem\u003eXanthomonas arboricola\u003c/em\u003e pv. \u003cem\u003epruni\u003c/em\u003e (Xap), poses a significant threat to the global peach industry. Studies have indicated that 41 Xap strains isolated from various peach cultivars in China exhibit moderate genetic differentiation, clear specificity to peach cultivars, and limited geographical differentiation. The genomic information of 36 Xap strains isolated from different areas has been deposited to the NCBI genome database; However, complete genome sequences for Xap strains identified in China remain lacking. In this study, the whole genome of the Xap 9-4 strain, isolated from diseased peach leaves in China, was assembled and annotated.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData description:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe genomic data of the Xap 9-4 strain were sequenced using the Illumina and PacBio platforms. The genome of Xap 9-4 consisted of a 5,174,371 bp circular chromosome and a 41,329 bp circular plasmid, encoding 4,660 protein-coding genes, 201 ncRNAs, 643 repeat regions and 7 prophages. Approximately 94.82% of the proteins were annotated. These findings will expand the genomic resources for Xap and provide a foundation for further studies on genetic diversity and pathogen-host interaction mechanisms.\u003c/p\u003e","manuscriptTitle":"Whole-genome sequence of Xanthomonas arboricola pv. pruni strain 9-4 causing peach bacterial spot in China","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-08 04:06:14","doi":"10.21203/rs.3.rs-7149576/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-09-05T16:01:31+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-13T14:08:52+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-10T02:20:40+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"253722290672180001954042859297997917271","date":"2025-08-06T04:55:25+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"36398391589869338990497233400431490784","date":"2025-08-05T16:31:22+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"39706006570537135672510825879705198706","date":"2025-08-05T12:44:21+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-08-05T11:01:06+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-07-28T11:27:01+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-07-28T11:26:50+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomic Data","date":"2025-07-17T13:25:09+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomic-data","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gtic","sideBox":"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gtic/default.aspx","title":"BMC Genomic Data","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"998be730-88f3-44d3-bd4f-aab67095c519","owner":[],"postedDate":"August 8th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-11-03T16:00:18+00:00","versionOfRecord":{"articleIdentity":"rs-7149576","link":"https://doi.org/10.1186/s12863-025-01377-4","journal":{"identity":"bmc-genomic-data","isVorOnly":false,"title":"BMC Genomic Data"},"publishedOn":"2025-10-29 15:57:16","publishedOnDateReadable":"October 29th, 2025"},"versionCreatedAt":"2025-08-08 04:06:14","video":"","vorDoi":"10.1186/s12863-025-01377-4","vorDoiUrl":"https://doi.org/10.1186/s12863-025-01377-4","workflowStages":[]},"version":"v1","identity":"rs-7149576","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7149576","identity":"rs-7149576","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}