First genomic analysis of a strain of Ralstonia pseudosolanacearum isolated from Mayotte island

First genomic analysis of a strain of Ralstonia pseudosolanacearum isolated from Mayotte island | 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 First genomic analysis of a strain of Ralstonia pseudosolanacearum isolated from Mayotte island Eva Caly-Simbou, Marie Veronique Nomenjanahary, Stéphanie Javegny, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7781192/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 08 Dec, 2025 Read the published version in BMC Genomic Data → Version 1 posted 9 You are reading this latest preprint version Abstract Objectives : The Ralstonia solanacearum species complex (RSSC) encompasses phytopathogenic bacteria responsible for bacterial wilt, a devastating disease affecting a wide range of agriculturally important crops. In the South-West Indian Ocean, lineage I-18 of R. pseudosolanacearum has emerged as a particularly destructive pathogen, posing a serious threat to regional food security. In this context, we report the complete genome sequence of isolate RUN2161, collected in Mayotte. This first genome from this island provides a valuable resource for unraveling the evolutionary and epidemiological mechanisms driving the emergence and spread of highly epidemic strains in agriculture. Data description : The genome of strain RUN2161 from Mayotte was sequenced using Illumina short reads and Nanopore long reads. A hybrid assembly was performed resulting in a complete genome of 5,989,529 bp with a G+C content of 66.7%. Functional annotation identified 5,268 CDS, 12 rRNAs, 61 tRNA genes, and 4 ncRNAs, assembled into one chromosome, one megaplasmid and one plasmid. Accessory plasmids are uncommon in RSSC. The RUN2161 plasmid contains Type IV secretion system genes, commonly found on conjugative plasmids, but less commonly, it also carries Type II secretion system genes involved in secretion of toxins and degradative enzymes, which could contribute to epidemiological success. Ralstonia solanacearum species complex Bacterial wilt South-West Indian Ocean Whole-genome sequencing Complete genome sequence Objective The Ralstonia solanacearum species complex ( RSSC ), responsible for bacterial wilt in many economically significant crops is distributed globally [1]. RSSC is a species complex divided into species and phylotypes, corresponding to their geographical origins: R. pseudosolanacearum from Asia (Phylotype I) and Africa (Phylotype III), R. solanacearum from Americas (Phylotype IIA and IIB), and R. syzygii from Indonesia-Australia (Phylotype IV) [2–4]. Within these phylotypes, 71 sequevars, based on the similarities in their nucleic sequence that encode egl gene have been defined so far [5]. In the South-West Indian Ocean region, the epidemiological distribution of the RSSC is particularly noteworthy. While phylotype I is dominant in this area [6], distinct prevalence patterns have been reported between sequevars I-18 and I-31. While I-31 strains are predominant in the small islands of this region as well as in East Africa [6–8], I-18 strains are strongly established in Madagascar [9, 10]. Interestingly, recent study highlights genomic diversity within the sequevar I-18 [10, 11]. In Mayotte Island, sequevar I-18 strains have been detected in agricultural fields, raising new concerns for local crop production [7]. Here, we present the first chromosome-level hybrid assembly of a Mahoran I-18 strain, isolated in 2012 from Solanum lycopersicum (tomato), in Dembeni in the east coast of Mayotte. Data description High molecular weight genomic DNA of R. pseudosolanacearum RUN2161 strain, was extracted using a protocol adapted for RSSC strains [11]. Samples were sequenced by the Genewiz-Azenta Laboratory platform (Leipzig, Germany) using Illumina NovaSeq technology. Long-read sequencing was performed using an R10.4.1 MinION flowcell and the SQK-RBK 114.96 Rapid Barcoding Kit (Oxford Nanopore Technology, UK). Basecalling was conducted with Dorado v0.9.0 [12] in the super accuracy mode. The genome assembly was performed using a hybrid pipeline [13]. Short reads and long reads were trimmed using Trimmomatic v0.39 [14] and Filtlong v0.2.1 [12], respectively. An initial hybrid assembly was generated with Unicycler v0.5.1 [15]. The assembly was first polished with long reads using four iterations of Racon v1.4.3 [16], followed by a second long-read polishing with Medaka v1.9.1 [17]. A third polishing step using short reads was performed with four iterations of NextPolish [18]. Finally, circularization of the replicons was carried out using Berokka v0.2.3 [12]. The complete genome assembly (DataSet 3; GCA_052747835.1), has a size of 5,989,529 bp. Assembly metrics and quality control, performed using Quast v.5.2.0 [19], BUSCO v.5.8.3 [20] and CheckM v.1.2.2 [21], revealed the high quality of this assembly with a very high level of completeness (99.8%) and no evidence of gene duplication or contamination (DataFile 1). The functional annotation was performed using the NCBI PGAP pipeline [22]. The entire genome encodes 5,161 coding genes and 77 RNAs (including 12 rRNAs, 61 tRNAs, and 4 ncRNAs) and comprise a circular chromosome of 3,758,906 bp with 66.7 % GC content and 3,403 coding genes, a megaplasmid of 2,178,702 bp with 66.5 % GC content and 1,692 coding genes, and a plasmid of 51,921 bp with 61.5 % GC content and 66 coding genes (DataSet 3, DataFile 2). Plasmids are not ubiquitous across RSSC and majority of those described are small (<50kb) [23, 24], although larger plasmids over 100 kb can also be found [25]. We screened the RUN2161 plasmid sequence against 864 RSSC genomes available in the NCBI database using BLASTN. Ten significant matches were identified, showing 63–87% nucleotide identity. Nine of these plasmids originated from phylotype I strains from China, South Korea, Thailand, and Israel, while one match corresponded to a phylotype IV strain from Indonesia (DataFile 3). The RUN2161 plasmid contains 66 genes, of which 41% correspond to hypothetical proteins with no assigned function. We reported Type IV secretion system (T4SS) genes and a toxin-antitoxin system that are commonly found on conjugative plasmids (DataFile 2). Surprisingly, the plasmid also carries three proteins associated with the type II secretion system (T2SS) of which an ATPase and a GspD protein. T2SS have been described as a major element implicated in toxins delivery including hydrolytic enzymes and toxins, including proteases, lipases. It often includes a cytoplasmic ATPase [26]. Interestingly, we have found two lytic transglycosylases, a phospholipase D and a peptidase S24. These enzymes, potentially secreted by the T2SS, are thus high valuable candidates to study the molecular mechanisms of virulence and epidemic success. 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) DataSet 1 Raw short Illumina sequencing reads 1 and 2 Sequence file (.fastq) NCBI Sequence Read Archive (https://identifiers.org/ncbi/insdc.sra:SRR35491076) [27] DataSet 2 Raw long nanopore sequencing reads Sequence file (.fastq) NCBI Sequence Read Archive (https://identifiers.org/ncbi/insdc.sra:SRR35404195) [28] DataSet 3 Complete genome and annotation of R. pseudosolanacearum RUN2161 GenBank/Annotation files NCBI GenBank (http://identifiers.org/assembly:GCA_052747835.1) [29] DataFile 1 Quality control of assembly (QUAST, BUSCO and CheckM) MS Excel file (.xlsx) Figshare, https://doi.org/10.6084/m9.figshare.30272398 [30] DataFile 2 Circular visualization of RUN2161 genome Portable Document Format file Figshare, https://doi.org/10.6084/m9.figshare.30273385 [31] DataFile 3 Alignments of plasmids Portable Document Format file Figshare, https://doi.org/10.6084/m9.figshare.30273451 [32] Limitations This study provides a high-quality genome assembly, combining short reads, which offer low error rates, with long reads, which enhance contiguity. This approach provides the best genome quality achievable with available technologies. However, the high genetic diversity of strains circulating in Mayotte highlights the need to investigate other genomes to gain a more comprehensive understanding of variability within RSSC . Moreover, genome annotation still requires improvement, as 18% of the predicted proteins remain of unknown function. Finally, functional validation of these candidate genes will be essential to fully understand their biological roles and potential implications. Abbreviations RSSC : Ralstonia solanacearum species complex T2SS: Type II secretion system T4SS: Type IV secretion system Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Availability of data and materials The genomic data described in this Data note can be freely and openly accessed on GenBank of NCBI under Bioproject accession PRJNA1328457 and BioSample accessions SAMN51336171. Raw Illumina and Nanopore reads were deposited under NCBI SRA accessions SRR35491076 and SRR35404195. The results of genome analysis have been uploaded to the Figshare repository. Please see Table 1 for details and links to data. Competing interests The authors declare no competing interests. Funding This Project is co-funded by the European Union and Région Réunion. Europe commits to Réunion through the ERDF fund 2024-1248-005756. This work is also supported by the French National Research Agency (ANR-JCJC BAOBAB, grant number: ANR-23-CE20-0031-01). Caly-Simbou E and Nomenjanahary MV received doctoral fellowships from the Conseil Régional de La Réunion, and CIRAD. Authors’ contributions Conceptualization, CSE, NMV, PY, SP, SRM; laboratory experiments, BC, CJJ, CSE, JS, NMV; computational genomic analyses, BC, CSE, PY; writing, CSE, PY, SP, SRM; supervision, PY, SP and SRM. The authors read and approved the final manuscript. 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Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24. https://doi.org/10.1093/nar/gkw569. Aoun N, Georgoulis SJ, Avalos JK, Grulla KJ, Miqueo K, Tom C, et al. A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia. mBio. 15:e00323-24. https://doi.org/10.1128/mbio.00323-24. Remenant B, Coupat-Goutaland B, Guidot A, Cellier G, Wicker E, Allen C, et al. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence. BMC Genomics. 2010;11:379. https://doi.org/10.1186/1471-2164-11-379. Ding S, Yu L, Lan G, Tang Y, Li Z, He Z, et al. Identification and genomic characterization of Ralstonia pseudosolanacearum strains isolated from pepino melon in China. Physiological and Molecular Plant Pathology. 2023;125:101977. https://doi.org/10.1016/j.pmpp.2023.101977. Korotkov KV, Sandkvist M. Architecture, Function, and Substrates of the Type II Secretion System. EcoSal Plus. 8:10.1128/ecosalplus.ESP-0034–2018. https://doi.org/10.1128/ecosalplus.esp-0034-2018. Caly-Simbou et al. DataSet 1. Raw short Illumina sequencing reads 1 and 2 of Ralstonia pseudosolanacearum RUN2161. Available from: https://identifiers.org/ncbi/insdc.sra:SRR35491076. Caly-Simbou et al. DataSet 2. Raw long nanopore sequencing reads of Ralstonia pseudosolanacearum RUN2161. Available from: https://identifiers.org/ncbi/insdc.sra:SRR35404195. Caly-Simbou et al. DataSet 3. Complete genome and annotation of Ralstonia pseudosolanacearum RUN2161. Available from: http://identifiers.org/assembly:GCA_052747835.1. Caly-Simbou et al. DataFile 1. Quality control of genome assembly of Ralstonia pseudosolanacearum RUN2161. Available from: https://doi.org/10.6084/m9.figshare.30272398. Caly-Simbou et al. DataFile 2. Circular visualization of Ralstonia pseudosolanacearum RUN2161 genome. Available from: https://doi.org/10.6084/m9.figshare.30273385. Caly-Simbou et al. DataFile 3. Alignments of plasmids. Available from: https://doi.org/10.6084/m9.figshare.30273385. Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 08 Dec, 2025 Read the published version in BMC Genomic Data → Version 1 posted Editorial decision: Revision requested 28 Oct, 2025 Reviews received at journal 28 Oct, 2025 Reviews received at journal 17 Oct, 2025 Reviewers agreed at journal 17 Oct, 2025 Reviewers agreed at journal 10 Oct, 2025 Reviewers invited by journal 09 Oct, 2025 Editor assigned by journal 08 Oct, 2025 Submission checks completed at journal 08 Oct, 2025 First submitted to journal 04 Oct, 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. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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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-7781192","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Data Note","associatedPublications":[],"authors":[{"id":524718642,"identity":"6b9f104a-b03a-47a4-9db6-96e2d544f912","order_by":0,"name":"Eva Caly-Simbou","email":"","orcid":"","institution":"University of Reunion Island","correspondingAuthor":false,"prefix":"","firstName":"Eva","middleName":"","lastName":"Caly-Simbou","suffix":""},{"id":524718643,"identity":"6eef7f79-2bed-485b-a31c-db364e51bd62","order_by":1,"name":"Marie Veronique Nomenjanahary","email":"","orcid":"","institution":"University of Reunion 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\u003cem\u003eR. solanacearum\u003c/em\u003e from Americas (Phylotype IIA and IIB), and \u003cem\u003eR. syzygii\u003c/em\u003e from Indonesia-Australia (Phylotype IV) [2\u0026ndash;4]. Within these phylotypes, 71 sequevars, based on the similarities in their nucleic sequence that encode egl gene have been defined so far [5].\u003c/p\u003e\n\u003cp\u003eIn the South-West Indian Ocean region, the epidemiological distribution of the \u003cem\u003eRSSC\u003c/em\u003e is particularly noteworthy. While phylotype I is dominant in this area [6], distinct prevalence patterns have been reported between sequevars I-18 and I-31. While I-31 strains are predominant in the small islands of this region as well as in East Africa [6\u0026ndash;8], I-18 strains are strongly established in Madagascar [9, 10]. Interestingly, recent study highlights genomic diversity within the sequevar I-18 [10, 11].\u003c/p\u003e\n\u003cp\u003eIn Mayotte Island, sequevar I-18 strains have been detected in agricultural fields, raising new concerns for local crop production [7]. Here, we present the first chromosome-level hybrid assembly of a Mahoran I-18 strain, isolated in 2012 from \u003cem\u003eSolanum lycopersicum\u003c/em\u003e (tomato), in Dembeni in the east coast of Mayotte.\u003c/p\u003e"},{"header":"Data description","content":"\u003cp\u003eHigh molecular weight genomic DNA of \u003cem\u003eR. pseudosolanacearum\u003c/em\u003e RUN2161 strain, was extracted using a protocol adapted for \u003cem\u003eRSSC\u003c/em\u003e strains [11]. Samples were sequenced by the Genewiz-Azenta Laboratory platform (Leipzig, Germany) using Illumina NovaSeq technology. Long-read sequencing was performed using an R10.4.1 MinION flowcell and the SQK-RBK 114.96 Rapid Barcoding Kit (Oxford Nanopore Technology, UK). Basecalling was conducted with Dorado v0.9.0 [12] in the super accuracy mode. The genome assembly was performed using a hybrid pipeline [13]. Short reads and long reads were trimmed using Trimmomatic v0.39 [14] and Filtlong v0.2.1 [12], respectively. An initial hybrid assembly was generated with Unicycler v0.5.1 [15]. The assembly was first polished with long reads using four iterations of Racon v1.4.3 [16], followed by a second long-read polishing with Medaka v1.9.1 [17]. A third polishing step using short reads was performed with four iterations of NextPolish [18]. Finally, circularization of the replicons was carried out using Berokka v0.2.3 [12].\u003c/p\u003e\n\u003cp\u003eThe complete genome assembly (DataSet 3; GCA_052747835.1), has a size of 5,989,529 bp. Assembly metrics and quality control, performed using Quast v.5.2.0 [19], BUSCO v.5.8.3 [20] and CheckM v.1.2.2 [21], revealed the high quality of this assembly with a very high level of completeness (99.8%) and no evidence of gene duplication or contamination (DataFile 1). The functional annotation was performed using the NCBI PGAP pipeline [22]. The entire genome encodes 5,161 coding genes and 77 RNAs (including 12 rRNAs, 61 tRNAs, and 4 ncRNAs) and comprise a circular chromosome of 3,758,906 bp with 66.7 % GC content and 3,403 coding genes, a megaplasmid of 2,178,702 bp with 66.5 % GC content and 1,692 coding genes, and a plasmid of 51,921 bp with 61.5 % GC content and 66 coding genes (DataSet 3, DataFile 2).\u003c/p\u003e\n\u003cp\u003ePlasmids are not ubiquitous across \u003cem\u003eRSSC\u003c/em\u003e and majority of those described are small (\u0026lt;50kb) [23, 24], although larger plasmids over 100 kb can also be found [25]. We screened the RUN2161 plasmid sequence against 864 \u003cem\u003eRSSC\u003c/em\u003e genomes available in the NCBI database using BLASTN. Ten significant matches were identified, showing 63\u0026ndash;87% nucleotide identity. Nine of these plasmids originated from phylotype I strains from China, South Korea, Thailand, and Israel, while one match corresponded to a phylotype IV strain from Indonesia (DataFile 3). The RUN2161 plasmid contains 66 genes, of which 41% correspond to hypothetical proteins with no assigned function. We reported Type IV secretion system (T4SS) genes and a toxin-antitoxin system that are commonly found on conjugative plasmids (DataFile 2).\u003c/p\u003e\n\u003cp\u003eSurprisingly, the plasmid also carries three proteins associated with the type II secretion system (T2SS) of which an ATPase and a GspD protein. T2SS have been described as a major element implicated in toxins delivery including hydrolytic enzymes and toxins, including proteases, lipases. It often includes a cytoplasmic ATPase [26]. Interestingly, we have found two lytic transglycosylases, a phospholipase D and a peptidase S24. These enzymes, potentially secreted by the T2SS, are thus high valuable candidates to study the molecular mechanisms of virulence and epidemic success.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 1\u003c/strong\u003e: Overview of data files/data sets.\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"650\" class=\"fr-table-selection-hover\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 11.2481%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eLabel\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 30.5085%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eName of data file/data set\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 24.8074%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eFile types\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003e(file extension)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 33.4361%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eData repository and identifier (DOI or accession number)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 11.2481%;\"\u003e\n \u003cp\u003eDataSet 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 30.5085%;\"\u003e\n \u003cp\u003eRaw short Illumina sequencing reads 1 and 2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 24.8074%;\"\u003e\n \u003cp\u003eSequence file (.fastq)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 33.4361%;\"\u003e\n \u003cp\u003eNCBI Sequence Read Archive (https://identifiers.org/ncbi/insdc.sra:SRR35491076)\u0026nbsp;[27]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 11.2481%;\"\u003e\n \u003cp\u003eDataSet 2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 30.5085%;\"\u003e\n \u003cp\u003eRaw long nanopore sequencing reads\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 24.8074%;\"\u003e\n \u003cp\u003eSequence file (.fastq)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 33.4361%;\"\u003e\n \u003cp\u003eNCBI Sequence Read Archive (https://identifiers.org/ncbi/insdc.sra:SRR35404195)\u0026nbsp;[28]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 11.2481%;\"\u003e\n \u003cp\u003eDataSet 3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 30.5085%;\"\u003e\n \u003cp\u003eComplete genome and annotation of \u003cem\u003eR. pseudosolanacearum\u003c/em\u003e RUN2161\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 24.8074%;\"\u003e\n \u003cp\u003eGenBank/Annotation files\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 33.4361%;\"\u003e\n \u003cp\u003eNCBI GenBank (http://identifiers.org/assembly:GCA_052747835.1)\u0026nbsp;[29]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 11.2481%;\"\u003e\n \u003cp\u003eDataFile 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 30.5085%;\"\u003e\n \u003cp\u003eQuality control of assembly (QUAST, BUSCO and CheckM)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 24.8074%;\"\u003e\n \u003cp\u003eMS Excel file (.xlsx)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 33.4361%;\"\u003e\n \u003cp\u003eFigshare, https://doi.org/10.6084/m9.figshare.30272398\u0026nbsp;[30]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 11.2481%;\"\u003e\n \u003cp\u003eDataFile 2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 30.5085%;\"\u003e\n \u003cp\u003eCircular visualization of RUN2161 genome\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 24.8074%;\"\u003e\n \u003cp\u003ePortable Document Format file\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 33.4361%;\"\u003e\n \u003cp\u003eFigshare, https://doi.org/10.6084/m9.figshare.30273385\u0026nbsp;[31]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 11.2481%;\"\u003e\n \u003cp\u003eDataFile 3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 30.5085%;\"\u003e\n \u003cp\u003eAlignments of plasmids\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 24.8074%;\"\u003e\n \u003cp\u003ePortable Document Format file\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 33.4361%;\"\u003e\n \u003cp\u003eFigshare, https://doi.org/10.6084/m9.figshare.30273451\u0026nbsp;[32]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e"},{"header":"Limitations","content":"\u003cp\u003eThis study provides a high-quality genome assembly, combining short reads, which offer low error rates, with long reads, which enhance contiguity. This approach provides the best genome quality achievable with available technologies. However, the high genetic diversity of strains circulating in Mayotte highlights the need to investigate other genomes to gain a more comprehensive understanding of variability within \u003cem\u003eRSSC\u003c/em\u003e. Moreover, genome annotation still requires improvement, as 18% of the predicted proteins remain of unknown function. Finally, functional validation of these candidate genes will be essential to fully understand their biological roles and potential implications.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003e\u003cem\u003eRSSC\u003c/em\u003e: \u003cem\u003eRalstonia solanacearum\u003c/em\u003e species complex\u003c/p\u003e\n\u003cp\u003eT2SS: Type II secretion system\u003c/p\u003e\n\u003cp\u003eT4SS: Type IV secretion system\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe genomic data described in this Data note can be freely and openly accessed on GenBank of NCBI under Bioproject accession PRJNA1328457 and BioSample accessions SAMN51336171. Raw Illumina and Nanopore reads were deposited under NCBI SRA accessions SRR35491076 and SRR35404195. The results of genome analysis have been uploaded to the Figshare repository. Please see Table 1 for details and links to data.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis Project is co-funded by the European Union and R\u0026eacute;gion R\u0026eacute;union. Europe commits to R\u0026eacute;union through the ERDF fund 2024-1248-005756. This work is also supported by the French National Research Agency (ANR-JCJC BAOBAB, grant number: ANR-23-CE20-0031-01). Caly-Simbou E and Nomenjanahary MV received doctoral fellowships from the Conseil R\u0026eacute;gional de La R\u0026eacute;union, and CIRAD.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026rsquo; contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eConceptualization, CSE, NMV, PY, SP, SRM; laboratory experiments, BC, CJJ, CSE, JS, NMV; computational genomic analyses, BC, CSE, PY; writing, CSE, PY, SP, SRM; supervision, PY, SP and SRM. The authors read and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgements\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors greatly acknowledge the Plant Protection Platform (3P, IBiSA).\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eLowe-Power TM, Avalos J, Bai Y, Munoz MC, Chipman K, Elmgreen VN, et al. 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Bioinformatics. 2013;29:1072\u0026ndash;5. https://doi.org/10.1093/bioinformatics/btt086.\u003c/li\u003e\n\u003cli\u003eManni M, Berkeley MR, Seppey M, Sim\u0026atilde;o FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021;38:4647\u0026ndash;54. https://doi.org/10.1093/molbev/msab199.\u003c/li\u003e\n\u003cli\u003eParks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043\u0026ndash;55. https://doi.org/10.1101/gr.186072.114.\u003c/li\u003e\n\u003cli\u003eTatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614\u0026ndash;24. https://doi.org/10.1093/nar/gkw569.\u003c/li\u003e\n\u003cli\u003eAoun N, Georgoulis SJ, Avalos JK, Grulla KJ, Miqueo K, Tom C, et al. A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia. mBio. 15:e00323-24. https://doi.org/10.1128/mbio.00323-24.\u003c/li\u003e\n\u003cli\u003eRemenant B, Coupat-Goutaland B, Guidot A, Cellier G, Wicker E, Allen C, et al. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence. BMC Genomics. 2010;11:379. https://doi.org/10.1186/1471-2164-11-379.\u003c/li\u003e\n\u003cli\u003eDing S, Yu L, Lan G, Tang Y, Li Z, He Z, et al. Identification and genomic characterization of \u003cem\u003eRalstonia pseudosolanacearum\u003c/em\u003e strains isolated from pepino melon in China. Physiological and Molecular Plant Pathology. 2023;125:101977. https://doi.org/10.1016/j.pmpp.2023.101977.\u003c/li\u003e\n\u003cli\u003eKorotkov KV, Sandkvist M. Architecture, Function, and Substrates of the Type II Secretion System. EcoSal Plus. 8:10.1128/ecosalplus.ESP-0034\u0026ndash;2018. https://doi.org/10.1128/ecosalplus.esp-0034-2018.\u003c/li\u003e\n\u003cli\u003eCaly-Simbou et al. DataSet 1. Raw short Illumina sequencing reads 1 and 2 of \u003cem\u003eRalstonia pseudosolanacearum\u003c/em\u003e RUN2161. Available from: https://identifiers.org/ncbi/insdc.sra:SRR35491076.\u003c/li\u003e\n\u003cli\u003eCaly-Simbou et al. DataSet 2. Raw long nanopore sequencing reads of \u003cem\u003eRalstonia pseudosolanacearum\u003c/em\u003e RUN2161. Available from: https://identifiers.org/ncbi/insdc.sra:SRR35404195.\u003c/li\u003e\n\u003cli\u003eCaly-Simbou et al. DataSet 3. Complete genome and annotation of \u003cem\u003eRalstonia pseudosolanacearum\u003c/em\u003e RUN2161. Available from: http://identifiers.org/assembly:GCA_052747835.1.\u003c/li\u003e\n\u003cli\u003eCaly-Simbou et al. DataFile 1. Quality control of genome assembly of \u003cem\u003eRalstonia pseudosolanacearum\u003c/em\u003e RUN2161. Available from: https://doi.org/10.6084/m9.figshare.30272398.\u003c/li\u003e\n\u003cli\u003eCaly-Simbou et al. DataFile 2. Circular visualization of \u003cem\u003eRalstonia pseudosolanacearum\u003c/em\u003e RUN2161 genome. Available from: https://doi.org/10.6084/m9.figshare.30273385.\u003c/li\u003e\n\u003cli\u003eCaly-Simbou et al. DataFile 3. Alignments of plasmids. Available from: https://doi.org/10.6084/m9.figshare.30273385.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"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":"Ralstonia solanacearum species complex, Bacterial wilt, South-West Indian Ocean, Whole-genome sequencing, Complete genome sequence","lastPublishedDoi":"10.21203/rs.3.rs-7781192/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7781192/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eObjectives\u003c/strong\u003e: The Ralstonia solanacearum species complex (RSSC) encompasses phytopathogenic bacteria responsible for bacterial wilt, a devastating disease affecting a wide range of agriculturally important crops. In the South-West Indian Ocean, lineage I-18 of R. pseudosolanacearum has emerged as a particularly destructive pathogen, posing a serious threat to regional food security. In this context, we report the complete genome sequence of isolate RUN2161, collected in Mayotte. This first genome from this island provides a valuable resource for unraveling the evolutionary and epidemiological mechanisms driving the emergence and spread of highly epidemic strains in agriculture.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData description\u003c/strong\u003e: The genome of strain RUN2161 from Mayotte was sequenced using Illumina short reads and Nanopore long reads. A hybrid assembly was performed resulting in a complete genome of 5,989,529 bp with a G+C content of 66.7%. Functional annotation identified 5,268 CDS, 12 rRNAs, 61 tRNA genes, and 4 ncRNAs, assembled into one chromosome, one megaplasmid and one plasmid. Accessory plasmids are uncommon in RSSC. The RUN2161 plasmid contains Type IV secretion system genes, commonly found on conjugative plasmids, but less commonly, it also carries Type II secretion system genes involved in secretion of toxins and degradative enzymes, which could contribute to epidemiological success.\u003c/p\u003e","manuscriptTitle":"First genomic analysis of a strain of Ralstonia pseudosolanacearum isolated from Mayotte island","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-10-07 09:02:56","doi":"10.21203/rs.3.rs-7781192/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-28T12:16:19+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-28T07:36:32+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-17T15:21:52+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"36398391589869338990497233400431490784","date":"2025-10-17T08:23:31+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"253722290672180001954042859297997917271","date":"2025-10-10T10:31:22+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-10-09T10:49:51+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-10-08T05:33:03+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-10-08T05:31:11+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomic Data","date":"2025-10-04T17:00:49+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":"0083f6a3-6830-4d8f-b0e3-d96d84547dbc","owner":[],"postedDate":"October 7th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-12-15T16:06:28+00:00","versionOfRecord":{"articleIdentity":"rs-7781192","link":"https://doi.org/10.1186/s12863-025-01395-2","journal":{"identity":"bmc-genomic-data","isVorOnly":false,"title":"BMC Genomic Data"},"publishedOn":"2025-12-08 15:57:56","publishedOnDateReadable":"December 8th, 2025"},"versionCreatedAt":"2025-10-07 09:02:56","video":"","vorDoi":"10.1186/s12863-025-01395-2","vorDoiUrl":"https://doi.org/10.1186/s12863-025-01395-2","workflowStages":[]},"version":"v1","identity":"rs-7781192","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7781192","identity":"rs-7781192","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}