Curtobacterium pruni sp. nov. causing black blotch on red apricot fruit in China

Curtobacterium pruni sp. nov. causing black blotch on red apricot fruit 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 Research Article Curtobacterium pruni sp. nov. causing black blotch on red apricot fruit in China Haiqing Yang, Jianbin Liu, Caige Lu, Le Liu, Ruiqi Wang, Piao Wu, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7415476/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 12 You are reading this latest preprint version Abstract The red apricot ( Prunus armeniaca ‘Bei-zhai-hong-xing’) is exclusively cultivated in Beijing and highly popular in the Chinese market due to its nutrient-rich fruits, which contain vitamin C, carotene, calcium, phosphorus, and potassium. In May 2021, distinct black spots or black botches were observed on fruits in many orchards and approximately 50% of fruits were infected, resulting in significant economic losses for farmers. Literature review confirmed no prior identification of the causal pathogen. Early-stage symptoms manifested as small, brown circular lesions that rapidly enlarged and turned black and formed black blotches within several days; no mycelia or spores were observed. Fruits exhibited high susceptibility, whereas leaves remained asymptomatic. Single colonies were isolated from diseased fruits. Representative isolate of Hongxing underwent pathogenicity testing and identification via morphological characterization and 16S rRNA gene phylogenetic analysis. Cells of the pathogen were rod-shaped, Gram-stain-positive, non-spore-forming and of (0.5-3.0) µm × (0.2–0.6) µm in size. The whole-genome sequencing of strain Hongxing showed that the circular chromosome comprised 3,884,414 bp with 70.98% G + C content and encoded 3,657 protein-coding genes. The phylogenomic comparison with other Curtobacterium species demonstrated that the strain Hongxing is distinctive from other known Curtobacterium species. Combined morphological and phylogenetic analyses identified strain Hongxing as a novel Curtobacterium species pathogenic to apricot fruit. We propose the novel species Curtobacterium pruni sp. nov., with type strain Hongxing T . To the best of our knowledge, this is the first report of Curtobacterium sp. as a pathogen on red apricot fruits. Curtobacterium pruni sp.nov. Prunus armeniaca phylogeny genome sequence Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Introduction Most Curtobacterium species are phytopathogens, causing diseases such as bacterial wilt of common bean (Wendland et al., 2016 ). However, certain strains of C. flaccumfaciens act as beneficial microbes that promote plant growth (Behrendt et al., 2002 ; Chase et al., 2017 ) and suppress plant diseases (Lacava et al., 2007 ). Curtobacterium flaccumfaciens pv. flaccumfaciens is a major pathogen of legumes, including common bean, soybean, and cowpea (Osdaghi, 2014; Harveson et al., 2015 ; Wendland et al., 2016 ; Sammer & Reiher, 2012 ). Bacterial wilt management is challenging due to the seedborne nature of Curtobacterium spp. and their persistence on weeds and crop debris in the field (Osdaghi et al., 2020 ; Nascimento et al., 2020 ). Recently described pathogens include Curtobacterium allii , the causal agent of onion bulb rot (Khanal et al., 2022 ). Rare human infections linked to Curtobacterium strains have also been documented (Francis et al., 2011 ), suggesting potential alternative hosts beyond plants. The red apricot ( Prunus armeniaca ‘Bei-zhai-hong-xing’) is highly popular in China for its thin-skinned, thick-fleshed fruits with small pits and high nutrient content (e.g., vitamin C, carotene, fructose, organic acids, protein, calcium, phosphorus, potassium). This cultivar is exclusively cultivated in Beijing’s Pinggu District due to specific geographic requirements and provides significant income for local farmers. In May 2020, distinct black blotches were observed on fruits in multiple orchards across Pinggu District, Beijing. Initial symptoms appeared as small, brown circular lesions that rapidly enlarged and blackened within days; no mycelia or spores were observed. Fruits exhibited high susceptibility, whereas leaves remained asymptomatic. Other local apricot cultivars showed lower infection rates. Approximately 50% of fruits in affected orchards were infected, causing substantial economic losses. A literature review indicated the causal agent was unidentified. This study characterizes the pathogen and establishes the taxonomic status of the causal pathogen. Materials and Methods Field samplings and pathogen isolation Diseased apricot fruits ( Prunus armeniaca ‘Bei-zhai-hong-xing’) were collected from orchards in Pinggu District, Beijing, China (40°01′N, 117°01′E). Five symptomatic fruits displaying typical black blotches were randomly sampled. Pathogen isolation followed Guarnaccia et al. ( 2021 ) with minor modifications. Symptomatic tissues (0.5–1.0 cm) from lesion margins were surface-disinfected in 70% ethanol (30 s), 1% sodium hypochlorite (30 s), rinsed in sterile distilled water, dried on sterile filter paper, and plated on Luria-Bertani agar (LBA). Plates were incubated at 25 ± 1°C for 48 h. Single colonies were re-streaked onto fresh LBA plates. After 48 h incubation, single colonies were re-isolated on LBA to obtain pure cultures. Twenty isolates were obtained; two (Hongxing and HX-A) were selected for molecular characterization (Table 1 ). Stock cultures were stored on LBA slants at 4°C for further study. Test of pathogenicity The pathogenicity was verified according to the procedures by Ogiso et al. (2002) with minor modifications. A bacterial suspension (10 4 CFU/mL) from pure cultures of the pathogen prepared from LB was sprayed onto five healthy apricot fruits ( Prunus armeniaca “Bei-zhai-hong-xing” ) in the orchard. The fruits inoculated with LB diluted by 10×fold with sterilized distilled water served as controls. Symptoms were recorded 7 days post-inoculation. Morphological Characterization Morphological characterization of the pathogen strains was carried out according to the methods described by Khanal et ac., (2022), with minor modifications.The pathogen strain was preliminarily identified by using morphological characteristics. The strain was inoculated on an LBA medium and observed for culture characters after incubation at 25°C for 48h. The strain cultured for 18–24 h on LBA plates was subjected to gram staining. Cell morphology was observed and photographed using an Olympus BX51 microscope. Biochemical tests were performed by using the API 50 CH Identification Kit. All the experiments were evaluated in triplicate to obtain accurate data. Molecular and Phylogenetic analysis The pathogen strain was further identified through the analysis of its 16S rRNA gene sequences. Briefly, the DNA of the strain was extracted by using the TIANamp bacterial DNA extraction kit and stored at 4°C. The 16S rDNA was amplified by polymerase chain reaction (PCR) with the bacterial universal primers 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′-GGTTACCTTGTTACGACTT-3′). The PCR reaction mixture contained 1 µL of DNA template, 5 µL of 10× PCR buffer, 4 µL of dNTPs (2.5 mmol/L), 3 µL of MgCl2 (25 mmol/L), 1 µLof each primer (1 mmol/L), 0.5 µL of Taq polymerase and 34.5 µL of ultrapure water. The reaction condition of 16S rDNA amplification was as follows: 94°C for 5 min; 30 cycles of 94°C for 1 min, 55°C for 30 s and 72°C for 1 min; and a final extension at 72°C for 10 min. Amplicons were electrophoresed on 1% agarose gels and sequenced (Beijing Tianyihuiyuan Biotechnology Co., Ltd.). DNA sequence homology searches were performed by using the online BLAST search engine in GenBank ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ). Phylogenetic trees were constructed from 16S rRNA sequences using MEGA7 (neighbor-joining method). Genome sequencing and genome annotation Genomic DNA was extracted using Wizard® Genomic DNA Purification Kit (Promega) according to manufacture’s protocol. Purified genomic DNA was quantified by TBS-380 fluorometer (Turner BioSystems Inc., Sunnyvale, CA). High quality DNA (OD260/280 = 1.8 ~ 2.0, >1µg) was used to do further research. For Illumina sequencing, at least 1µg genomic DNA was used for each strain in sequencing library construction. DNA was sheared (400–500 bp) using a Covaris M220 (per manufacturer’s protocol).. Illumina sequencing libraries were prepared from the sheared fragments using the NEXTflex™ Rapid DNA-Seq Kit. Briefly, 5’ prime ends were first end-repaired and phosphorylated. Next, the 3’ ends were A-tailed and ligated to sequencing adapters. The third step is to enrich the adapters-ligated products using PCR. The prepared libraries then were used for paired-end Illumina sequencing (2 × 150 bp) on an Illumina HiSeq X Ten machine. Bioinformatics analyses used Majorbio Cloud Platform ( www.majorbio.com ). The original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ file. Those FASTQ files are the original data provided for users, and they include the detailed read sequences and the read quality information. A statistic of quality information was applied for quality trimming, by which the low quality data can be removed to form clean data. An assembly of the clean reads were performed using SOAPdenovo2 (Koren et al., 2017 ). Glimmer (Delcher et al., 2007 ) was used for CDS prediction, tRNA-scan-SE (Borodovsky et al., 1993) was used for tRNA prediction and Barrnap was used for rRNA prediction. The predicted CDSs were annotated from NR, Swiss-Prot, Pfam, GO, COG and KEGG database using sequence alignment tools such as BLASTP, Diamond and HMMER. Briefly, each set of query proteins were aligned with the databases, and annotations of best-matched subjects (e-value < 10 − 5 ) were obtained for gene annotation. The phylogeny based on the whole genome data was determined by calculating the average nucleotide identity with closely related Curtobacterium species with the Orthologous Average Nucleotide Identity Tool (OrthoANI)(Lee et al., 2016 ). Genome-based taxonomy was analyzed using TYGS ( https://tygs.dsmz.de ; Meier-Kolthoff & Göker, 2019 ). Results and Discussion Field survey and pathogen isolation Most of apricot fruits were infected by Curtobacterium sp., and showed the typical black blotches (Fig. 1 ). Diseased fruits were collected and totally 20 isolates were obtained and showed the same morphology of colones on LBA plates (Fig. 2 ). Two pure cultures, respectively designated Hongxing and HX-A, were selected for further analysis (Table 1 ). Table 1 Two typical strains of the pathogen isolated from the diseased red apricot fruits Strains Color and shapes of colonies GenBank NO. of 16s rRNA gene Hongxing T Yellow, round, and smooth surface OP721100 HX-A Yellow, round, and smooth surface OP614835.1 Test of pathogenicity By 7 days post-inoculation (dpi), symptoms of black sunken lesions identical to field infections appeared on inoculated fruits (Fig. 3 a). At 14 days post inoculation, the typical black blotches were enlarged and the fruits become yellow in color (Fig. 3 b). In this experiment, in the control groups where the the fruits were inoculated inoculated with LB diluted by 10×fold with sterilized distilled, no black blotches was observed on fruits at 7 days (Fig. 3 c) or 14 days (Fig. 3 d) post inoculation. The results showed that the strains used for inoculation are the pathogen which caused the black blotch on red apricots in the orchards, and the pathogenicity of the pathogen on red apricots was confirmed. Morphological Characterization The colony of the pathogen strain Hongxing was round or oval, ivory off-yellow and nontransparent with an smooth surface, and had a white round spot in the middle on LBA plates after 48 h of growth. Under microscope with 100× magnification, the cells of strain Hongxing was rod-shaped, Gram-stain-positive, non-spore-forming and of (0.5-3.0) µm × (0.2–0.6) µm in size (Fig. 4 ), the morphology characterization is consistent to the genus Curtobacterium described by Yamada and Komagata (1972). Molecular and Phylogenetic analysis Morphological characterizations were further confirmed by phylogenetic analysis of the sequences of 16S rRNA gene. Sequence data were deposited to the NCBI (Table 1 ). Comparison of 16S rRNA gene sequences with the nucleotide database of DDBJ/EMBL/GenBank using BLASTn search revealed that the strain Hongxing and strain HX-A were placed into a single clade, and are different from other known species of the genus Curtobacterium . The results of phylogeny analysis suggested that the strain Hongxing and the strain HX-A belongs to a novel species of the genus Curtobacterium (Fig. 5 ). Genome sequencing and genome annotation The genome assembly of Hongxing consisted of 1 contig larger than 1 Kbp, with a total size of 3,884,414 bp and mean GC content 70.76%. The genome of Hongxing possesses 3657 genes and encodes at least 12 rRNAs, 10 sRNA and 40 tRNAs (Table 2 and Fig. 6 ). The genome of the strain Hongxing also harbored genes related to cell mobility and defense mechanisms (Fig. 6 and Fig. 7 ). The analysis of the amino sequences of the whole genome by the software showed that the pathogen belongs to the bacteria of Type III secretion system (T3SS). Genome sequence phylogenies showed that the strain Hongxing is closely related species of Curtobacterium flaccumfaciens CFBP 3418 and Curtobacterium flaccumfaciens LMG 3645 (type strains), respectively and that the strain Hongxing presented dDDH values of 66.2% with the latter species. The phylogeny analysis of the whole genomes of strain Hongxing and other known species of the genus Curtobacterium sp. revealed that the strains Hongxing and HX-A belonged to a novel species and formed a single clade in the phylogenetic tree (Fig. 8 ), suggesting that the pathogen causing black blotches on apricot fruits is a novel disease pathogen. Table 2 General genomic features of Curtobacterium sp. strain Hongxing Feature Hongxing Genome size (bp) 3,884,414 Number of genes 3657 Number of RNAs 62 Longest contig 3,884,414 bp GC content (%) 70.76 N50 3,884,414 bp N75 3,884,414 bp L50 1 L75 1 Phylogenetic analysis of the whole genome Genome sequence phylogenies showed that the strain Hongxing is closely related species of C. flaccumfaciens CFBP 3418 and C. aurantiacum CFBP 8819 (Fig. 8 ). The results of the digital DNA-DNA hybridization showed that dDDH of the genomes of strain Hongxing and C. flaccumfaciens CFBP 3418 and C. aurantiacum CFBP 8819 were 57.7% (d6) and 54.9% (d6), respectively, which were lower than 70%, confirming that the strain Hongxing was a novel species of the genus Curtobacterium (Table 3 ). Table 3 The results of the digital DNA-DNA hybridization of the genomes of strain Hongxing and Curtobacterium spp.* Query strain Subject strain dDDH (d0, in %) C.I. (d0, in %) dDDH (d4, in %) C.I. (d4, in %) dDDH (d6, in %) C.I. (d6, in %) G + C content difference (in %) Hongxing C. flaccumfaciens CFBP 3418 66.2 [62.4–69.9] 33.7 [31.3–36.3] 57.7 [54.5–60.9] 0.2 Hongxing C. flaccumfaciens LMG 3645 66.2 [62.4–69.9] 33.7 [31.3–36.2] 57.7 [54.5–60.8] 0.22 Hongxing C. aurantiacum CFBP 8819 62.7 [58.9–66.3] 33.3 [30.9–35.8] 54.9 [51.8–58.0] 0.09 Hongxing C. allii 20TX0166 61.2 [57.5–64.8] 33.3 [30.9–35.8] 53.8 [50.7–56.9] 0.02 Hongxing C. pusillum ATCC 19096 49.8 [46.4–53.2] 28.2 [25.9–30.7] 43.3 [40.3–46.3] 0.09 Hongxing C. caseinilyticum GDMCC 1.2667 45.8 [42.5–49.3] 26.3 [23.9–28.7] 39.6 [36.6–42.6] 1.18 Hongxing C. albidum DSM 20512 44 [40.6–47.4] 26.3 [23.9–28.8] 38.3 [35.4–41.4] 1.15 Hongxing C. citreum JCM 1345 44.1 [40.7–47.5] 26.1 [23.8–28.6] 38.3 [35.4–41.4] 1.26 Hongxing C. luteum DSM 20542 46.5 [43.1–49.9] 26.1 [23.7–28.6] 40 [37.0–43.0] 0.92 Hongxing C. luteum JCM 1480 46.5 [43.1–49.9] 26 [23.6–28.5] 39.9 [36.9–43.0] 0.99 Hongxing C. guangdongense RRHDQ66 45.9 [42.5–49.4] 25.8 [23.5–28.3] 39.5 [36.5–42.5] 0.22 Hongxing C. aetherium L6-1 36.7 [33.3–40.2] 25.3 [22.9–27.7] 32.8 [29.9–35.9] 1.25 Hongxing C. herbarum DSM 14013 37.4 [34.0–40.9] 25.2 [22.9–27.7] 33.3 [30.3–36.4] 0.66 Hongxing C. salicis WW7 38.3 [34.9–41.8] 24.5 [22.2–27.0] 33.7 [30.7–36.8] 0.61 Hongxing C. ammoniigenes NBRC 101786 17.6 [14.5–21.1] 20.3 [18.0–22.7] 17.3 [14.7–20.3] 2.91 Hongxing C. plantarum LMG 16222 12.5 [9.8–15.8] 19 [16.8–21.4] 12.9 [10.6–15.7] 15.72 * The genome of strain Hongxing was subject to the website of https://tygs.dsmz.de/ for digital DNA-DNA hybridization analysis to further confirm the taxonomy of the causal pathogen. Conclusion This research described the pathogen causing novel disease of black blotches on apricot fruits in China, and based on morphology characterization and the results of the phylogenetic tree analysis16S rRNA gene sequence and the genome sequences, the pathogen was identified as a novel species of the genus Curtobacterium sp.. Summarizing the morphology and molecular characterization, the novel species Curtobacterium pruni sp. nov., was proposed. Although some species of the genus Curtobacterium have been well documented as a common plant pathogen with the potential to cause significant disease in many legumes, to the best of our knowledge, this is the first report of Curtobacterium sp. as a pathogen on red apricot fruits. Declarations Authors' contributions Conception and design of the study: D.P. Zhang and J.B. Liu. Performed experiments: H.Q. Yang and R.Q. Wang. Analyzed data: C.G. Lu, Y. Yang, L. Liu. Wrote the manuscript: Y. Yang, P. Wu, D.P. Zhang. All authors read and approved the final manuscript. Acknowledgments The authors thank the project of National Key R&D Program of China（Grant number ：2024YFD1501304） Funding This project was supported by National Key R&D Program of China（Grant number ：2024YFD1501304）. Conflict of interest The Authors declare that they have no conflict of interest. Compliance with ethical standards This article does not contain any studies with animals performed by any of the authors. This article does not contain any studies with human participants or animals performed by any of the authors. Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. References Fujinaga M, Yamagishi N, Ogiso H, Takeuchi J, Moriwaki J, Sato T (2011) First report of celery stunt anthracnose caused by Colletotrichum simmondsii in Japan. J Gen Plant Pathol 77:243–247. 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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-7415476","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":506734056,"identity":"e1a6f29c-ece5-49fe-8a26-f5689f800689","order_by":0,"name":"Haiqing Yang","email":"","orcid":"","institution":"Fruit industry office of Pinggu district","correspondingAuthor":false,"prefix":"","firstName":"Haiqing","middleName":"","lastName":"Yang","suffix":""},{"id":506734058,"identity":"42840f26-ca5e-4202-adcd-205a419773eb","order_by":1,"name":"Jianbin Liu","email":"","orcid":"","institution":"Beijing Academy of Agriculture and Forestry Science","correspondingAuthor":false,"prefix":"","firstName":"Jianbin","middleName":"","lastName":"Liu","suffix":""},{"id":506734059,"identity":"8288a445-09c6-498c-93f6-cfb90d324aaf","order_by":2,"name":"Caige Lu","email":"","orcid":"","institution":"Beijing Academy of Agriculture and Forestry Science","correspondingAuthor":false,"prefix":"","firstName":"Caige","middleName":"","lastName":"Lu","suffix":""},{"id":506734060,"identity":"b1c0343e-bcc1-4027-a838-f0adf237c4a3","order_by":3,"name":"Le Liu","email":"","orcid":"","institution":"Fruit industry office of Pinggu district","correspondingAuthor":false,"prefix":"","firstName":"Le","middleName":"","lastName":"Liu","suffix":""},{"id":506734061,"identity":"a630c8a9-3413-4723-808c-bb7394e188f2","order_by":4,"name":"Ruiqi Wang","email":"","orcid":"","institution":"Fruit industry office of Pinggu district","correspondingAuthor":false,"prefix":"","firstName":"Ruiqi","middleName":"","lastName":"Wang","suffix":""},{"id":506734063,"identity":"cf16cf78-0a34-4097-b21e-1ec28b656db1","order_by":5,"name":"Piao Wu","email":"","orcid":"","institution":"Mudanjiang Normal University","correspondingAuthor":false,"prefix":"","firstName":"Piao","middleName":"","lastName":"Wu","suffix":""},{"id":506734065,"identity":"cdf7ede1-eb3c-48b1-bab6-a69ddda8cdc8","order_by":6,"name":"Yue Yang","email":"","orcid":"","institution":"Shenyang Normal University","correspondingAuthor":false,"prefix":"","firstName":"Yue","middleName":"","lastName":"Yang","suffix":""},{"id":506734066,"identity":"0ef7c637-8f22-422c-b972-1a697e5d13ce","order_by":7,"name":"Dianpeng Zhang","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA20lEQVRIiWNgGAWjYDCCAzAGe/PBBwkVNkRrMWBg4DmWbPDgTBopWiRy1CQfth0irIPv9uGDn278+SNv3pDDVpHAdoCBv707Aa8WyXNpydK5bQaGcw6cPXYjgecOg8SZsxvwajE4w2MgndtgwDiDsS/tRoLEMwYDiVxCWvg//875Y2A/g5nHrCDB4DAxWnjYpHPYDBJnsPGYMSQkEKFF8gybmXVum3HyDB62ZImEA2k8BP3Cd4b58e2cP3K2M+QfH/z485+NHH97L34tGICHNOWjYBSMglEwCrACAEm3S6GqJgotAAAAAElFTkSuQmCC","orcid":"","institution":"Beijing Academy of Agriculture and Forestry Science","correspondingAuthor":true,"prefix":"","firstName":"Dianpeng","middleName":"","lastName":"Zhang","suffix":""}],"badges":[],"createdAt":"2025-08-20 08:53:43","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7415476/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7415476/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":90594050,"identity":"577620d4-cbe5-4645-9654-8c3d1a06205f","added_by":"auto","created_at":"2025-09-04 13:20:40","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":427807,"visible":true,"origin":"","legend":"\u003cp\u003eSymptoms of black blotch disease on apricot (\u003cem\u003eP. armeniaca\u003c/em\u003e ‘Bei-zhai-hong-xing’) in Pinggu District orchards: (a) Field view of infected fruits with black blotches; (b) Close-up of lesions on fruit\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/2d8dfd0c77435a7971dcd729.png"},{"id":90594051,"identity":"5a83e303-dfec-4d19-899d-661004438e82","added_by":"auto","created_at":"2025-09-04 13:20:40","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":354048,"visible":true,"origin":"","legend":"\u003cp\u003eRepresentative colonies of the isolated pathogen cultured on Luria-Bertani agar (LBA) at 25 ±1°C for 48 h\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/3bb41f2b0146d8b7c3c31078.png"},{"id":90594052,"identity":"c4b09d8b-b359-4bee-a798-c92450ac5b1b","added_by":"auto","created_at":"2025-09-04 13:20:40","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":417676,"visible":true,"origin":"","legend":"\u003cp\u003eTypical symptoms of black blotches on apricot fruits after inoculation of the pathogen strain Hongxing: (a) symptoms of black blotches on fruits at 7 days post inoculation of the pathogen;(b) symptoms of black blotches on fruits at 14 days post inoculation of the pathogen; (c) and (d) no symptoms of black blotches observed on fruits in control groups where the fruits were inoculated with LB diluted by 10×fold with sterilized distilled\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/61f8b4321a200b07b96148fe.png"},{"id":90595541,"identity":"4231dddd-5bb8-44c9-a802-ee75c7a92bb9","added_by":"auto","created_at":"2025-09-04 13:36:40","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":475262,"visible":true,"origin":"","legend":"\u003cp\u003eMorphology and Colony of the pathogen strain Hongxing: (a) colony of Hongxing grown on LBA plate at 25℃for 48 h; (b) Gram staining of Hongxing cells photoed under microscope. Bars strand 10 μm.\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/b3a377a7c8c7582f562ed2de.png"},{"id":90595543,"identity":"2a718c40-a782-421b-aa17-6a2ee2f1d6f8","added_by":"auto","created_at":"2025-09-04 13:36:40","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":145249,"visible":true,"origin":"","legend":"\u003cp\u003eMaximum likely-hood phylogenetic tree constructed using the 16S rRNA gene sequence of strain Hongxing of \u003cem\u003eCurtobacterium\u003c/em\u003e isolated from a diseased apricot fruit, and the sequences of closely related species of the genus\u003cem\u003e Curtobacterium\u003c/em\u003e. The phylogenetic tree was constructed by the software MEGA v. 7.0, and bootstrap values at the branching nodes indicate the percentage of 1000 replicates. The scale bar refers to the number of nucleotide substitutions per site. The superscript\u003csup\u003e T\u003c/sup\u003e denotes the type strain of the species used and the GenBank accession number of each strain is in parentheses\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/b9058aaa44e2cc0f8755b6fa.png"},{"id":90596430,"identity":"9bb92aff-7498-4c96-b0e6-394f3d3841c5","added_by":"auto","created_at":"2025-09-04 13:44:40","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":138369,"visible":true,"origin":"","legend":"\u003cp\u003eGenome map of the pathogen strain Hongxing\u003c/p\u003e","description":"","filename":"6.png","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/5918258fd698a5c6dd5746d7.png"},{"id":90594056,"identity":"48aeb336-862c-40d5-b870-2d115663eecd","added_by":"auto","created_at":"2025-09-04 13:20:40","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":74252,"visible":true,"origin":"","legend":"\u003cp\u003eCO function classification of the genome of strain Hongxing\u003c/p\u003e","description":"","filename":"7.png","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/a187c9b5f8ae55811027b54c.png"},{"id":90594054,"identity":"e698d069-0d85-428a-9cda-7e2b206f725b","added_by":"auto","created_at":"2025-09-04 13:20:40","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":74389,"visible":true,"origin":"","legend":"\u003cp\u003eThe phylogeny based on the whole genome data was determined by the Type (Strain) Genome Server (TYGS), a free bioinformatics platform available under \u003ca href=\"https://tygs.dsmz.de/\"\u003ehttps://tygs.dsmz.de\u003c/a\u003e. The phylogenetic tree inferred with FastME 2.1.6.1 from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values \u0026gt; 60 % from 1000 replications, with an average branch support of 98.9 %.\u003c/p\u003e","description":"","filename":"8.png","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/f022f49a8a03baeae09cdf1a.png"},{"id":90596832,"identity":"006bb868-0db1-447f-bfb3-2eed39d92629","added_by":"auto","created_at":"2025-09-04 13:52:41","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3172039,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7415476/v1/997830d2-ccff-4911-9bcc-473da4a40035.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Curtobacterium pruni sp. nov. causing black blotch on red apricot fruit in China","fulltext":[{"header":"Introduction","content":"\u003cp\u003eMost \u003cem\u003eCurtobacterium\u003c/em\u003e species are phytopathogens, causing diseases such as bacterial wilt of common bean (Wendland et al., \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). However, certain strains of \u003cem\u003eC. flaccumfaciens\u003c/em\u003e act as beneficial microbes that promote plant growth (Behrendt et al., \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2002\u003c/span\u003e; Chase et al., \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2017\u003c/span\u003e) and suppress plant diseases (Lacava et al., \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2007\u003c/span\u003e). \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e pv. flaccumfaciens is a major pathogen of legumes, including common bean, soybean, and cowpea (Osdaghi, 2014; Harveson et al., \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Wendland et al., \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Sammer \u0026amp; Reiher, \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). Bacterial wilt management is challenging due to the seedborne nature of \u003cem\u003eCurtobacterium\u003c/em\u003e spp. and their persistence on weeds and crop debris in the field (Osdaghi et al., \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Nascimento et al., \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Recently described pathogens include \u003cem\u003eCurtobacterium allii\u003c/em\u003e, the causal agent of onion bulb rot (Khanal et al., \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). Rare human infections linked to \u003cem\u003eCurtobacterium\u003c/em\u003e strains have also been documented (Francis et al., \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2011\u003c/span\u003e), suggesting potential alternative hosts beyond plants.\u003c/p\u003e\u003cp\u003eThe red apricot (\u003cem\u003ePrunus armeniaca\u003c/em\u003e \u0026lsquo;Bei-zhai-hong-xing\u0026rsquo;) is highly popular in China for its thin-skinned, thick-fleshed fruits with small pits and high nutrient content (e.g., vitamin C, carotene, fructose, organic acids, protein, calcium, phosphorus, potassium). This cultivar is exclusively cultivated in Beijing\u0026rsquo;s Pinggu District due to specific geographic requirements and provides significant income for local farmers. In May 2020, distinct black blotches were observed on fruits in multiple orchards across Pinggu District, Beijing. Initial symptoms appeared as small, brown circular lesions that rapidly enlarged and blackened within days; no mycelia or spores were observed. Fruits exhibited high susceptibility, whereas leaves remained asymptomatic. Other local apricot cultivars showed lower infection rates. Approximately 50% of fruits in affected orchards were infected, causing substantial economic losses. A literature review indicated the causal agent was unidentified. This study characterizes the pathogen and establishes the taxonomic status of the causal pathogen.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003eField samplings and pathogen isolation\u003c/h2\u003e\u003cp\u003eDiseased apricot fruits (\u003cem\u003ePrunus armeniaca\u003c/em\u003e \u0026lsquo;Bei-zhai-hong-xing\u0026rsquo;) were collected from orchards in Pinggu District, Beijing, China (40\u0026deg;01\u0026prime;N, 117\u0026deg;01\u0026prime;E). Five symptomatic fruits displaying typical black blotches were randomly sampled. Pathogen isolation followed Guarnaccia et al. (\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2021\u003c/span\u003e) with minor modifications. Symptomatic tissues (0.5\u0026ndash;1.0 cm) from lesion margins were surface-disinfected in 70% ethanol (30 s), 1% sodium hypochlorite (30 s), rinsed in sterile distilled water, dried on sterile filter paper, and plated on Luria-Bertani agar (LBA). Plates were incubated at 25\u0026thinsp;\u0026plusmn;\u0026thinsp;1\u0026deg;C for 48 h. Single colonies were re-streaked onto fresh LBA plates. After 48 h incubation, single colonies were re-isolated on LBA to obtain pure cultures. Twenty isolates were obtained; two (Hongxing and HX-A) were selected for molecular characterization (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Stock cultures were stored on LBA slants at 4\u0026deg;C for further study.\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eTest of pathogenicity\u003c/h3\u003e\n\u003cp\u003eThe pathogenicity was verified according to the procedures by Ogiso et al. (2002) with minor modifications. A bacterial suspension (10\u003csup\u003e4\u003c/sup\u003e CFU/mL) from pure cultures of the pathogen prepared from LB was sprayed onto five healthy apricot fruits (\u003cem\u003ePrunus armeniaca\u003c/em\u003e \u0026ldquo;Bei-zhai-hong-xing\u0026rdquo; ) in the orchard. The fruits inoculated with LB diluted by 10\u0026times;fold with sterilized distilled water served as controls. Symptoms were recorded 7 days post-inoculation.\u003c/p\u003e\n\u003ch3\u003eMorphological Characterization\u003c/h3\u003e\n\u003cp\u003eMorphological characterization of the pathogen strains was carried out according to the methods described by Khanal et ac., (2022), with minor modifications.The pathogen strain was preliminarily identified by using morphological characteristics. The strain was inoculated on an LBA medium and observed for culture characters after incubation at 25\u0026deg;C for 48h. The strain cultured for 18\u0026ndash;24 h on LBA plates was subjected to gram staining. Cell morphology was observed and photographed using an Olympus BX51 microscope. Biochemical tests were performed by using the API 50 CH Identification Kit. All the experiments were evaluated in triplicate to obtain accurate data.\u003c/p\u003e\n\u003ch3\u003eMolecular and Phylogenetic analysis\u003c/h3\u003e\n\u003cp\u003eThe pathogen strain was further identified through the analysis of its 16S rRNA gene sequences. Briefly, the DNA of the strain was extracted by using the TIANamp bacterial DNA extraction kit and stored at 4\u0026deg;C. The 16S rDNA was amplified by polymerase chain reaction (PCR) with the bacterial universal primers 27F (5\u0026prime;-AGAGTTTGATCCTGGCTCAG-3\u0026prime;) and 1492R (5\u0026prime;-GGTTACCTTGTTACGACTT-3\u0026prime;). The PCR reaction mixture contained 1 \u0026micro;L of DNA template, 5 \u0026micro;L of 10\u0026times; PCR buffer, 4 \u0026micro;L of dNTPs (2.5 mmol/L), 3 \u0026micro;L of MgCl2 (25 mmol/L), 1 \u0026micro;Lof each primer (1 mmol/L), 0.5 \u0026micro;L of Taq polymerase and 34.5 \u0026micro;L of ultrapure water. The reaction condition of 16S rDNA amplification was as follows: 94\u0026deg;C for 5 min; 30 cycles of 94\u0026deg;C for 1 min, 55\u0026deg;C for 30 s and 72\u0026deg;C for 1 min; and a final extension at 72\u0026deg;C for 10 min. Amplicons were electrophoresed on 1% agarose gels and sequenced (Beijing Tianyihuiyuan Biotechnology Co., Ltd.). DNA sequence homology searches were performed by using the online BLAST search engine in GenBank (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://blast.ncbi.nlm.nih.gov/Blast.cgi\u003c/span\u003e\u003cspan address=\"http://blast.ncbi.nlm.nih.gov/Blast.cgi\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). Phylogenetic trees were constructed from 16S rRNA sequences using MEGA7 (neighbor-joining method).\u003c/p\u003e\n\u003ch3\u003eGenome sequencing and genome annotation\u003c/h3\u003e\n\u003cp\u003eGenomic DNA was extracted using Wizard\u0026reg; Genomic DNA Purification Kit (Promega) according to manufacture\u0026rsquo;s protocol. Purified genomic DNA was quantified by TBS-380 fluorometer (Turner BioSystems Inc., Sunnyvale, CA). High quality DNA (OD260/280\u0026thinsp;=\u0026thinsp;1.8\u0026thinsp;~\u0026thinsp;2.0, \u0026gt;1\u0026micro;g) was used to do further research.\u003c/p\u003e\u003cp\u003eFor Illumina sequencing, at least 1\u0026micro;g genomic DNA was used for each strain in sequencing library construction. DNA was sheared (400\u0026ndash;500 bp) using a Covaris M220 (per manufacturer\u0026rsquo;s protocol).. Illumina sequencing libraries were prepared from the sheared fragments using the NEXTflex\u0026trade; Rapid DNA-Seq Kit. Briefly, 5\u0026rsquo; prime ends were first end-repaired and phosphorylated. Next, the 3\u0026rsquo; ends were A-tailed and ligated to sequencing adapters. The third step is to enrich the adapters-ligated products using PCR. The prepared libraries then were used for paired-end Illumina sequencing (2 \u0026times; 150 bp) on an Illumina HiSeq X Ten machine. Bioinformatics analyses used Majorbio Cloud Platform (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ewww.majorbio.com\u003c/span\u003e\u003cspan address=\"http://www.majorbio.com\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eThe original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ file. Those FASTQ files are the original data provided for users, and they include the detailed read sequences and the read quality information. A statistic of quality information was applied for quality trimming, by which the low quality data can be removed to form clean data. An assembly of the clean reads were performed using SOAPdenovo2 (Koren et al., \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2017\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eGlimmer (Delcher et al., \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2007\u003c/span\u003e) was used for CDS prediction, tRNA-scan-SE (Borodovsky et al., 1993) was used for tRNA prediction and Barrnap was used for rRNA prediction. The predicted CDSs were annotated from NR, Swiss-Prot, Pfam, GO, COG and KEGG database using sequence alignment tools such as BLASTP, Diamond and HMMER. Briefly, each set of query proteins were aligned with the databases, and annotations of best-matched subjects (e-value\u0026thinsp;\u0026lt;\u0026thinsp;10\u003csup\u003e\u0026minus;\u0026thinsp;5\u003c/sup\u003e) were obtained for gene annotation.\u003c/p\u003e\u003cp\u003eThe phylogeny based on the whole genome data was determined by calculating the average nucleotide identity with closely related Curtobacterium species with the Orthologous Average Nucleotide Identity Tool (OrthoANI)(Lee et al., \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). Genome-based taxonomy was analyzed using TYGS (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://tygs.dsmz.de\u003c/span\u003e\u003cspan address=\"https://tygs.dsmz.de\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e; Meier-Kolthoff \u0026amp; G\u0026ouml;ker, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2019\u003c/span\u003e).\u003c/p\u003e"},{"header":"Results and Discussion","content":"\u003cdiv id=\"Sec9\" class=\"Section2\"\u003e\u003ch2\u003eField survey and pathogen isolation\u003c/h2\u003e\u003cp\u003eMost of apricot fruits were infected by \u003cem\u003eCurtobacterium\u003c/em\u003e sp., and showed the typical black blotches (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Diseased fruits were collected and totally 20 isolates were obtained and showed the same morphology of colones on LBA plates (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Two pure cultures, respectively designated Hongxing and HX-A, were selected for further analysis (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\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\u003eTwo typical strains of the pathogen isolated from the diseased red apricot fruits\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"3\"\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\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eStrains\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eColor and shapes of colonies\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003eGenBank NO. of 16s rRNA gene\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003csup\u003eT\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eYellow, round, and smooth surface\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eOP721100\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHX-A\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eYellow, round, and smooth surface\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eOP614835.1\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eTest of pathogenicity\u003c/h3\u003e\n\u003cp\u003eBy 7 days post-inoculation (dpi), symptoms of black sunken lesions identical to field infections appeared on inoculated fruits (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ea). At 14 days post inoculation, the typical black blotches were enlarged and the fruits become yellow in color (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eb). In this experiment, in the control groups where the the fruits were inoculated inoculated with LB diluted by 10\u0026times;fold with sterilized distilled, no black blotches was observed on fruits at 7 days (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ec) or 14 days (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ed) post inoculation. The results showed that the strains used for inoculation are the pathogen which caused the black blotch on red apricots in the orchards, and the pathogenicity of the pathogen on red apricots was confirmed.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\u003ch2\u003eMorphological Characterization\u003c/h2\u003e\u003cp\u003eThe colony of the pathogen strain Hongxing was round or oval, ivory off-yellow and nontransparent with an smooth surface, and had a white round spot in the middle on LBA plates after 48 h of growth. Under microscope with 100\u0026times; magnification, the cells of strain Hongxing was rod-shaped, Gram-stain-positive, non-spore-forming and of (0.5-3.0) \u0026micro;m \u0026times; (0.2\u0026ndash;0.6) \u0026micro;m in size (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e), the morphology characterization is consistent to the genus \u003cem\u003eCurtobacterium\u003c/em\u003e described by Yamada and Komagata (1972).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e\u003ch2\u003eMolecular and Phylogenetic analysis\u003c/h2\u003e\u003cp\u003eMorphological characterizations were further confirmed by phylogenetic analysis of the sequences of 16S rRNA gene. Sequence data were deposited to the NCBI (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Comparison of 16S rRNA gene sequences with the nucleotide database of DDBJ/EMBL/GenBank using BLASTn search revealed that the strain Hongxing and strain HX-A were placed into a single clade, and are different from other known species of the genus \u003cem\u003eCurtobacterium\u003c/em\u003e. The results of phylogeny analysis suggested that the strain Hongxing and the strain HX-A belongs to a novel species of the genus \u003cem\u003eCurtobacterium\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e\u003ch2\u003eGenome sequencing and genome annotation\u003c/h2\u003e\u003cp\u003eThe genome assembly of Hongxing consisted of 1 contig larger than 1 Kbp, with a total size of 3,884,414 bp and mean GC content 70.76%. The genome of Hongxing possesses 3657 genes and encodes at least 12 rRNAs, 10 sRNA and 40 tRNAs (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e and Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). The genome of the strain Hongxing also harbored genes related to cell mobility and defense mechanisms (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e \u003cb\u003eand\u003c/b\u003e Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). The analysis of the amino sequences of the whole genome by the software showed that the pathogen belongs to the bacteria of Type III secretion system (T3SS).\u003c/p\u003e\u003cp\u003eGenome sequence phylogenies showed that the strain Hongxing is closely related species of Curtobacterium flaccumfaciens CFBP 3418 and \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e LMG 3645 (type strains), respectively and that the strain Hongxing presented dDDH values of 66.2% with the latter species. The phylogeny analysis of the whole genomes of strain Hongxing and other known species of the genus \u003cem\u003eCurtobacterium\u003c/em\u003e sp. revealed that the strains Hongxing and HX-A belonged to a novel species and formed a single clade in the phylogenetic tree (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003e), suggesting that the pathogen causing black blotches on apricot fruits is a novel disease pathogen.\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eGeneral genomic features of \u003cem\u003eCurtobacterium\u003c/em\u003e sp. strain Hongxing\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"3\"\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\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eFeature\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eGenome size (bp)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e3,884,414\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eNumber of genes\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e3657\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eNumber of RNAs\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e62\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eLongest contig\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e3,884,414 bp\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eGC content (%)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e70.76\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eN50\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e3,884,414 bp\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eN75\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e3,884,414 bp\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eL50\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eL75\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec14\" class=\"Section2\"\u003e\u003ch2\u003ePhylogenetic analysis of the whole genome\u003c/h2\u003e\u003cp\u003eGenome sequence phylogenies showed that the strain Hongxing is closely related species of \u003cem\u003eC. flaccumfaciens\u003c/em\u003e CFBP 3418 and \u003cem\u003eC. aurantiacum\u003c/em\u003e CFBP 8819 (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003e). The results of the digital DNA-DNA hybridization showed that dDDH of the genomes of strain Hongxing and \u003cem\u003eC. flaccumfaciens\u003c/em\u003e CFBP 3418 and \u003cem\u003eC. aurantiacum\u003c/em\u003e CFBP 8819 were 57.7% (d6) and 54.9% (d6), respectively, which were lower than 70%, confirming that the strain Hongxing was a novel species of the genus \u003cem\u003eCurtobacterium\u003c/em\u003e (Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eThe results of the digital DNA-DNA hybridization of the genomes of strain Hongxing and Curtobacterium spp.*\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"9\"\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=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c9\" colnum=\"9\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eQuery strain\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eSubject strain\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003edDDH\u003c/p\u003e\u003cp\u003e(d0, in %)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eC.I. (d0, in %)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e\u003cp\u003edDDH\u003c/p\u003e\u003cp\u003e(d4, in %)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c6\"\u003e\u003cp\u003eC.I. (d4, in %)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c7\"\u003e\u003cp\u003edDDH\u003c/p\u003e\u003cp\u003e(d6, in %)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c8\"\u003e\u003cp\u003eC.I. (d6, in %)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c9\"\u003e\u003cp\u003eG\u0026thinsp;+\u0026thinsp;C content difference (in %)\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. flaccumfaciens CFBP 3418\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e66.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[62.4\u0026ndash;69.9]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e33.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[31.3\u0026ndash;36.3]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e57.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[54.5\u0026ndash;60.9]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. flaccumfaciens LMG 3645\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e66.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[62.4\u0026ndash;69.9]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e33.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[31.3\u0026ndash;36.2]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e57.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[54.5\u0026ndash;60.8]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.22\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. aurantiacum CFBP 8819\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e62.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[58.9\u0026ndash;66.3]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e33.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[30.9\u0026ndash;35.8]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e54.9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[51.8\u0026ndash;58.0]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.09\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. allii 20TX0166\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e61.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[57.5\u0026ndash;64.8]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e33.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[30.9\u0026ndash;35.8]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e53.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[50.7\u0026ndash;56.9]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.02\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. pusillum ATCC 19096\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e49.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[46.4\u0026ndash;53.2]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e28.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[25.9\u0026ndash;30.7]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e43.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[40.3\u0026ndash;46.3]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.09\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. caseinilyticum GDMCC 1.2667\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e45.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[42.5\u0026ndash;49.3]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e26.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[23.9\u0026ndash;28.7]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e39.6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[36.6\u0026ndash;42.6]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e1.18\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. albidum DSM 20512\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e44\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[40.6\u0026ndash;47.4]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e26.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[23.9\u0026ndash;28.8]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e38.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[35.4\u0026ndash;41.4]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e1.15\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. citreum JCM 1345\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e44.1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[40.7\u0026ndash;47.5]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e26.1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[23.8\u0026ndash;28.6]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e38.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[35.4\u0026ndash;41.4]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e1.26\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. luteum DSM 20542\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e46.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[43.1\u0026ndash;49.9]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e26.1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[23.7\u0026ndash;28.6]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e40\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[37.0\u0026ndash;43.0]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.92\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. luteum JCM 1480\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e46.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[43.1\u0026ndash;49.9]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e26\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[23.6\u0026ndash;28.5]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e39.9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[36.9\u0026ndash;43.0]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.99\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. guangdongense RRHDQ66\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e45.9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[42.5\u0026ndash;49.4]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e25.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[23.5\u0026ndash;28.3]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e39.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[36.5\u0026ndash;42.5]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.22\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. aetherium L6-1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e36.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[33.3\u0026ndash;40.2]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e25.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[22.9\u0026ndash;27.7]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e32.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[29.9\u0026ndash;35.9]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e1.25\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. herbarum DSM 14013\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e37.4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[34.0\u0026ndash;40.9]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e25.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[22.9\u0026ndash;27.7]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e33.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[30.3\u0026ndash;36.4]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.66\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. salicis WW7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e38.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[34.9\u0026ndash;41.8]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e24.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[22.2\u0026ndash;27.0]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e33.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[30.7\u0026ndash;36.8]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e0.61\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. ammoniigenes NBRC 101786\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e17.6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[14.5\u0026ndash;21.1]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e20.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[18.0\u0026ndash;22.7]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e17.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[14.7\u0026ndash;20.3]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e2.91\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHongxing\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eC. plantarum LMG 16222\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e12.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e[9.8\u0026ndash;15.8]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e19\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e[16.8\u0026ndash;21.4]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e12.9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e\u003cp\u003e[10.6\u0026ndash;15.7]\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e\u003cp\u003e15.72\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003e* The genome of strain Hongxing was subject to the website of \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://tygs.dsmz.de/\u003c/span\u003e\u003cspan address=\"https://tygs.dsmz.de/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e for digital DNA-DNA hybridization analysis to further confirm the taxonomy of the causal pathogen.\u003c/p\u003e\u003c/div\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThis research described the pathogen causing novel disease of black blotches on apricot fruits in China, and based on morphology characterization and the results of the phylogenetic tree analysis16S rRNA gene sequence and the genome sequences, the pathogen was identified as a novel species of the genus \u003cem\u003eCurtobacterium\u003c/em\u003e sp.. Summarizing the morphology and molecular characterization, the novel species \u003cem\u003eCurtobacterium pruni\u003c/em\u003e sp. nov., was proposed. Although some species of the genus \u003cem\u003eCurtobacterium\u003c/em\u003e have been well documented as a common plant pathogen with the potential to cause significant disease in many legumes, to the best of our knowledge, this is the first report of \u003cem\u003eCurtobacterium\u003c/em\u003e sp. as a pathogen on red apricot fruits.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAuthors\u0026apos; contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eConception and design of the study: D.P. Zhang and J.B. Liu.\u003c/p\u003e\n\u003cp\u003ePerformed experiments: H.Q. Yang and R.Q. Wang.\u003c/p\u003e\n\u003cp\u003eAnalyzed data: C.G. Lu, Y. Yang, L. Liu.\u003c/p\u003e\n\u003cp\u003eWrote the manuscript: Y. Yang, P. Wu, D.P. Zhang.\u003c/p\u003e\n\u003cp\u003eAll authors read and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgments\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors thank the project of National Key R\u0026amp;D Program of China（Grant number\u0026nbsp;：2024YFD1501304）\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis project was supported by National Key R\u0026amp;D Program of China（Grant number\u0026nbsp;：2024YFD1501304）.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of interest\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThe Authors declare that they have no conflict of interest.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompliance with ethical standards\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis article does not contain any studies with animals performed by any of the authors. This article does not contain any studies with human participants or animals performed by any of the authors.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003eFujinaga M, Yamagishi N, Ogiso H, Takeuchi J, Moriwaki J, Sato T (2011) First report of celery stunt anthracnose caused by \u003cem\u003eColletotrichum simmondsii\u0026nbsp;\u003c/em\u003ein Japan. J Gen Plant Pathol 77:243\u0026ndash;247.\u003c/li\u003e\n \u003cli\u003eGuarnaccia V, Martino I, Gilardil G, Garibaldi A, Gullino ML (2021) \u003cem\u003eColletotrichum\u003c/em\u003e spp. causing anthracnose on ornamental plants in northern Italy. J Plant Pathol 103:127\u0026ndash;137.\u003c/li\u003e\n \u003cli\u003eFarris JS. Estimating phylogenetic trees from distance matrices. Am Nat. 1972;106: 645\u0026ndash;667.\u003c/li\u003e\n \u003cli\u003eMeier-Kolthoff JP, G\u0026ouml;ker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat. Commun. 2019;10: 2182.\u003c/li\u003e\n \u003cli\u003eWendland E, Nascimento RM, Ferreira LM, Souza EJ, Maccheroni W Jr (2016) First report of \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e pv. flaccumfaciens causing bacterial wilt of common bean in Brazil. Plant Dis 100:414.\u003c/li\u003e\n \u003cli\u003eBehrendt U, Munch JC, Kottke I, Berg G (2002) Endophytic bacteria isolated from roots of field-grown maize (Zea mays L.) enhance the growth of canola (Brassica napus L.) seedlings under gnotobiotic conditions. Biol Fertil Soils 36:112\u0026ndash;117.\u003c/li\u003e\n \u003cli\u003eChase AJ, Beattie GA, Goodfellow M (2017) Diversity and plant growth-promoting traits of culturable endophytic bacteria isolated from field-grown maize (Zea mays L.). Plant Soil 418:191\u0026ndash;206.\u003c/li\u003e\n \u003cli\u003eLacava PT, Azevedo JL, Maccheroni W Jr, Ara\u0026uacute;jo WL, Monteiro RV (2007) Endophytic bacteria isolated from coffee plants (Coffea arabica L.) promote growth and protect against phytopathogens. Res Microbiol 158:86 - 93.\u003c/li\u003e\n \u003cli\u003eOsdaghi E, Kharazmi M, Ghorbani M (2014) First report of \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e pv. flaccumfaciens causing bacterial wilt of common bean in Iran. Plant Dis 98:437.\u003c/li\u003e\n \u003cli\u003eHarveson RM, Osborne LD, Wrather JA (2015) First report of \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e pv. flaccumfaciens causing bacterial wilt of soybean in Nebraska. Plant Dis 99:1026.\u003c/li\u003e\n \u003cli\u003eWendland E, Nascimento RM, Ferreira LM, Souza EJ, Maccheroni W Jr (2016) First report of \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e pv. flaccumfaciens causing bacterial wilt of common bean in Brazil. Plant Dis 100:414.\u003c/li\u003e\n \u003cli\u003eSammer U, Reiher H (2012) First report of \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e pv. flaccumfaciens causing bacterial wilt of common bean in Germany. Plant Dis 96:1821.\u003c/li\u003e\n \u003cli\u003eOsdaghi E, Kharazmi M, Mohammadi M, Safaraei-Mahroo S, Bahar M (2020) Management of \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e pv. flaccumfaciens, the causal agent of common bean bacterial wilt. Arch Phytopathol Plant Prot 53:869\u0026ndash;884.\u003c/li\u003e\n \u003cli\u003eNascimento RM, Lopes AR, Souza EJ, Maccheroni W Jr, Wendland E (2020) Detection of \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e pv. flaccumfaciens in common bean seeds by loop-mediated isothermal amplification (LAMP). Eur J Plant Pathol 156:493\u0026ndash;502.\u003c/li\u003e\n \u003cli\u003eKhanal S, Adhikari B, Adhikari K, Shrestha R, Chhetri P, Gautam R (2022) First report of onion bulb rot caused by \u003cem\u003eCurtobacterium allii\u003c/em\u003e in Nepal. Plant Dis 106:2404.\u003c/li\u003e\n \u003cli\u003eFrancis KP, Chitnis SS, Srinivasan V, Narayanan S, Krishnan S (2011) \u003cem\u003eCurtobacterium flaccumfaciens\u003c/em\u003e subsp. flaccumfaciens bacteremia in a patient with acute myeloid leukemia. J Clin Microbiol 49:820 - 822.\u003c/li\u003e\n \u003cli\u003eGuarnaccia V, Martino I, Gilardi G, Garibaldi A, Gullino ML (2021) \u003cem\u003eColletotrichum\u003c/em\u003e spp. causing anthracnose on ornamental plants in northern Italy. J Plant Pathol 103:127\u0026ndash;137.\u003c/li\u003e\n \u003cli\u003eKhanal S, Adhikari B, Adhikari K, Shrestha R, Chhetri P, Gautam R (2022) First report of onion bulb rot caused by \u003cem\u003eCurtobacterium allii\u003c/em\u003e in Nepal. Plant Dis 106:2404.\u003c/li\u003e\n \u003cli\u003eKoren S, Schatz MC, Walenz BP (2017) Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation. Genome Research 27:722 - 736.\u003c/li\u003e\n \u003cli\u003eDelcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673\u0026ndash;679.\u003c/li\u003e\n \u003cli\u003eLee JH, Ouk Kim Y, Park S, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100\u0026ndash;1103.\u003c/li\u003e\n \u003cli\u003eMeier-Kolthoff JP, G\u0026ouml;ker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10:2182.\u003c/li\u003e\n \u003cli\u003eYamada K, Komagata K (1972) Transfer of Microbacterium flaccumfaciens (ex Hylemon et al. 1963) comb. nov. and Microbacterium testaceum (ex Stapp 1940) comb. nov. to the genus \u003cem\u003eCurtobacterium\u003c/em\u003e. International Journal of Systematic Bacteriology 22 (3):335 - 345.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"antonie-van-leeuwenhoek","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"anto","sideBox":"Learn more about [Antonie van Leeuwenhoek](https://www.springer.com/journal/10482)","snPcode":"10482","submissionUrl":"https://submission.nature.com/new-submission/10482/3","title":"Antonie van Leeuwenhoek","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Curtobacterium pruni sp.nov., Prunus armeniaca, phylogeny, genome sequence","lastPublishedDoi":"10.21203/rs.3.rs-7415476/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7415476/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe red apricot (\u003cem\u003ePrunus armeniaca\u003c/em\u003e \u0026lsquo;Bei-zhai-hong-xing\u0026rsquo;) is exclusively cultivated in Beijing and highly popular in the Chinese market due to its nutrient-rich fruits, which contain vitamin C, carotene, calcium, phosphorus, and potassium. In May 2021, distinct black spots or black botches were observed on fruits in many orchards and approximately 50% of fruits were infected, resulting in significant economic losses for farmers. Literature review confirmed no prior identification of the causal pathogen. Early-stage symptoms manifested as small, brown circular lesions that rapidly enlarged and turned black and formed black blotches within several days; no mycelia or spores were observed. Fruits exhibited high susceptibility, whereas leaves remained asymptomatic. Single colonies were isolated from diseased fruits. Representative isolate of Hongxing underwent pathogenicity testing and identification via morphological characterization and 16S rRNA gene phylogenetic analysis. Cells of the pathogen were rod-shaped, Gram-stain-positive, non-spore-forming and of (0.5-3.0) \u0026micro;m \u0026times; (0.2\u0026ndash;0.6) \u0026micro;m in size. The whole-genome sequencing of strain Hongxing showed that the circular chromosome comprised 3,884,414 bp with 70.98% G\u0026thinsp;+\u0026thinsp;C content and encoded 3,657 protein-coding genes. The phylogenomic comparison with other \u003cem\u003eCurtobacterium\u003c/em\u003e species demonstrated that the strain Hongxing is distinctive from other known \u003cem\u003eCurtobacterium\u003c/em\u003e species. Combined morphological and phylogenetic analyses identified strain Hongxing as a novel \u003cem\u003eCurtobacterium\u003c/em\u003e species pathogenic to apricot fruit. We propose the novel species \u003cem\u003eCurtobacterium pruni\u003c/em\u003e sp. nov., with type strain Hongxing\u003csup\u003eT\u003c/sup\u003e. To the best of our knowledge, this is the first report of \u003cem\u003eCurtobacterium\u003c/em\u003e sp. as a pathogen on red apricot fruits.\u003c/p\u003e","manuscriptTitle":"Curtobacterium pruni sp. nov. causing black blotch on red apricot fruit in China","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-04 13:20:35","doi":"10.21203/rs.3.rs-7415476/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-21T13:57:01+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-20T19:10:27+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"247574754141815816819776972040985785067","date":"2025-10-20T02:20:14+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-17T07:27:57+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"24012814536959463700370042796028110940","date":"2025-10-14T04:06:54+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"209343839603642520138435212605144089147","date":"2025-10-14T01:18:18+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"100385161227114780894624910532789114622","date":"2025-10-13T06:59:10+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"252676308004804507885465597834157221184","date":"2025-10-01T08:58:16+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-08-28T06:57:34+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-08-21T08:19:41+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-21T08:17:38+00:00","index":"","fulltext":""},{"type":"submitted","content":"Antonie van Leeuwenhoek","date":"2025-08-20T08:51:01+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"antonie-van-leeuwenhoek","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"anto","sideBox":"Learn more about [Antonie van Leeuwenhoek](https://www.springer.com/journal/10482)","snPcode":"10482","submissionUrl":"https://submission.nature.com/new-submission/10482/3","title":"Antonie van Leeuwenhoek","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"a87548ca-9fda-41ad-ae4e-1b9f26e5e055","owner":[],"postedDate":"September 4th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[],"tags":[],"updatedAt":"2025-10-21T14:08:20+00:00","versionOfRecord":[],"versionCreatedAt":"2025-09-04 13:20:35","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7415476","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7415476","identity":"rs-7415476","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}