High-Quality Genome Resource of Mango Bacterial Black Spot Pathogen Xanthomonas Citri Pv. Mangiferaeindicae GXG07 Isolated from Guangxi, China

HomePlant DiseaseVol. 106, No. 3High-Quality Genome Resource of Mango Bacterial Black Spot Pathogen Xanthomonas citri pv. mangiferaeindicae GXG07 Isolated from Guangxi, China PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseHigh-Quality Genome Resource of Mango Bacterial Black Spot Pathogen Xanthomonas citri pv. mangiferaeindicae GXG07 Isolated from Guangxi, ChinaFengzhi Bie, Yiming Li, Zhibin Liu, Meijing Qin, Shuping Li, Xue Dan, Sheng Huang, Yong-Qiang He, and Wei JiangFengzhi BieState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaSearch for more papers by this author, Yiming LiState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, ChinaSearch for more papers by this author, Zhibin LiuState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaSearch for more papers by this author, Meijing QinState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaSearch for more papers by this author, Shuping LiState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaSearch for more papers by this author, Xue DanState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, ChinaSearch for more papers by this author, Sheng HuangState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaSearch for more papers by this author, Yong-Qiang He†Corresponding authors: W. Jiang; E-mail Address: weijiang@gxu.edu.cn, and Y.-Q. He; E-mail Address: yqhe@gxu.edu.cnhttps://orcid.org/0000-0001-6803-0431State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, ChinaSearch for more papers by this author, and Wei Jiang†Corresponding authors: W. Jiang; E-mail Address: weijiang@gxu.edu.cn, and Y.-Q. He; E-mail Address: yqhe@gxu.edu.cnState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, ChinaSearch for more papers by this author AffiliationsAuthors and Affiliations Fengzhi Bie1 Yiming Li1 2 Zhibin Liu1 Meijing Qin1 Shuping Li1 Xue Dan1 2 Sheng Huang1 Yong-Qiang He1 2 † Wei Jiang1 † 1State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China 2National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China Published Online:8 Mar 2022https://doi.org/10.1094/PDIS-08-21-1714-AAboutSectionsView articlePDFPDF Plus ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleGenome AnnouncementXanthomonas citri pv. mangiferaeindicae is the causal agent of mango bacterial black spot (MBBS), which is present in many mango-growing regions and leads to great economic losses to the mango industry. Due to the limitation of high-quality genomic resources, little is known about the molecular pathogenesis of X. citri pv. mangiferaeindicae. Here, we used PacBio High Fidelity reads (HiFi) sequencing technology to sequence and analyze the whole genome of X. citri pv. mangiferaeindicae strain GXG07 isolated from Guangxi, the largest mango-growing region in China.Mango (Mangifera indica L.), belonging to the Anacardiaceae family, is one of the major special flavor fruit in tropical and subtropical areas and one of the most important fruits in the Guangxi region, China. In recent years, MBBS, also called mango bacterial canker or angular leaf spot, was observed increasingly in most mango yards in Guangxi, which led to huge economic losses in both mango planting and processing. The causal agent of MBBS, X. citri pv. mangiferaeindicae, was first isolated in South Africa (Doidge 1915), then reported in tropical and subtropical mango-producing areas of India, Pakistan, Brazil, Philippines, China, and the United States (Gagnevin and Pruvost 2001; Gagnevin et al. 1997; Patel et al. 1948). X. citri pv. mangiferaeindicae can infect mango leaves, fruit, branches, and trunk, resulting in a significant reduction in mango yield and quality, and decline in vitality of the evergreen tree. Genomic analysis is currently the most powerful tool for genetic assays and biological research; however, few complete genome sequences are available in X. citri pv. mangiferaeindicae. To date, three strains of X. citri pv. mangiferaeindicae whose genomes were sequenced have been reported: the LMG 941 strain from India (Midha et al. 2012); XC01 strain from Guangxi, China (Liu et al. 2018); and L242 from the United States (Dommel et al. 2019). However, there are obvious contradictions and inconsistency among the three genomes, because the genome sizes of strains LMG 941, XC01, and L242 are 5.11 Mb (Midha et al. 2012), 3.86 Mb (Liu et al. 2018), and 5.30 Mb (Dommel et al. 2019), respectively. Strikingly, in the first two genomes, there is no information about the transcription activator-like effector (TALE) genes, the important virulence and avirulence genes in most pathovars of X. citri (An et al. 2020). For strain LM941, because the genome was sequenced on the Roche 454 GS (FLX Titanium) pyrosequencing platform, it is reasonable that the highly repetitive TALE gene sequences were not correctly assembled. However, for strain XC01, the correctness of the extremely small genome in X. citri pv. mangiferaeindicae deserves further consideration. Here, we reported the complete genome sequence for strain GXG07 generated by long-read sequencing.In summer 2020, X. citri pv. mangiferaeindicae strain GXG07 was isolated and purified from a diseased leaf of M. indica L. ‘Guire 7’, a major mango cultivar in Baise, Guangxi Autonomous Region, the largest mango-growing area in China. GXG07 can produce typical black necrosis on mango leaves by artificial inoculation. Molecular identification showed that the 16S ribosomal DNA sequence of GXG07 is 99.9% of that of strain LMG 941, the characterized X. citri pv. mangiferaeindicae strain (Midha et al. 2012), suggesting that GXG07 belongs to X. citri pv. mangiferaeindicae. To sequence the whole genome of GXG07, its total DNA was obtained and purified by using Qiagen Genomic-tip 20G. The average fragment length of the sequencing library is about 15 kb and the sequencing was performed using the PacBio Sequel II System (Pacific Biosciences) at Biomarker Technologies Co., Ltd. (Beijing, China). In total, 250,505 reads and 2,393,214,969 bp were obtained. N50 length was 10,307 bp and mean coverage for the strain GXG07 genome was about 450×. The HiFi reads have been de novo assembled by using the Hifiasm software (Cheng et al. 2021). The Pilon v1.22 software was used to correct the assembly with Illumina data, and Circulator v1.5.5 software was used to cyclize and adjust the starting site. Three circular contigs were assembled and the two smaller contigs contained parA, trwB, and trwC, the plasmid-related genes, revealing their plasmid identity (Niu et al. 2015). CheckM v1.1.3 identified an average of 99.52% genome completeness and an average contamination of 0.00%, using the Xanthomonas genus-level taxonomic marker set (Parks et al. 2015). Thus, the genome of strain GXG07 contained a chromosome and two plasmids, with sizes of 5,166,537, 79,634, and 30,169 bp, respectively (Table 1). Phylogenetic analysis (Zuo and Hao 2015) based on genome sequences of some sequenced Xanthomonas strains indicated that GXG07 but not XC01 is clearly clustered with other X. citri pv. mangiferaeindicae strains in the clade of the species of X. citri (Fig. 1). Values of average nucleotide identity of strain GXG07 compared with LG81-27 and LMG 941 were 99.79 and 99.87%, respectively, which exceed the generally accepted 95% cut-off level for taxonomy affiliation of newly sequenced genomes (Richter et al. 2016). Functional annotation of the three assembled contigs was done using Prodigal v2.6.3 (Hyatt D et al. 2010). The predicted genes encode 4,871 proteins, 54 transfer RNAs, 6 ribosomal RNAs, and 278 other noncoding RNAs. The strain GXG07 genome encodes typical pathogenicity and virulence factors found in Xanthomonas spp. (An et al. 2020), including extracellular hydrolases, extracellular polysaccharides, adhesins, type II secretion system, type III secretion system, and type III-secreted effectors (T3SEs) (An et al. 2020; Dommel et al. 2019). Of the T3SEs, 10 TALEs were annotated to be encoded in the genome, which belong to TalED, TalIL, TalIT, TalIU, TalIV TalIW, TalIX, TalIY, TalIZ, and TalJA classes based on the patterns of the repeat variable diresidue (RVD) in the central domain of each TALE (Grau et al. 2016) (Table 2). The strain GXG07 genome provides gene resources for elucidating the biology and pathogenicity of the phytopathogen and developing new strategies for controlling mango bacterial black spot.Table 1. Genomic features of X. citri pv. mangiferaeindicae strain GXG07 and other sequenced X. citri pv. mangiferaeindicae strainsaStrainsGenome featuresGXG07LMG 941bXC01cLG56-10dLG81-27dDE0062dGenome size (bp)Chromosome5,166,5375,111,5373,865,1655,255,9845,107,0116,002,465Plasmid-1(pGXG07-1) 79,634NoNo16,24171,216NoPlasmid-2(pGXG07-2) 30,169NoNo4,81822,906NoG+C content (%)64.6964.8568.9364.5864.7257.20Coding density (%)86.08−89.55−−−Genes4,8714,4203,3744,5554,4935,586Coding sequences4,5334,1133,1734,4644,4025,502Transfer RNA545052505073Ribosomal RNA64641418Noncoding RNA2782151393838−TALE genes100000−Average CDS length1,001−1,006−−−aAbbreviations: TALE = transcription activator-like effector, CDS = coding sequence, and − indicates data not available.bData from Midha et al. (2012).cData from Liu et al. (2018).dGenomic data from NCBI (https://www.ncbi.nlm.nih.gov/genome/). There is no detailed genome data of strain L242 published (Dommel et al. 2019).Table 1. Genomic features of X. citri pv. mangiferaeindicae strain GXG07 and other sequenced X. citri pv. mangiferaeindicae strainsaView as image HTML Fig. 1. Phylogenetic analysis of Xanthomonas citri pv. mangiferaeindicae GXG07 based on genome sequences of representative Xanthomonas strains. Genome sequences were obtained from NCBI (https://www.ncbi.nlm.nih.gov/genome/). The tree was annotated and visualized by using the CVTree3 web server (http://cvtree.online/v3/cvtree/) and phylogenetic trees by using the neighbor-joining method. K-tuple length is 6 (Zuo and Hao 2015). The “X” indicates the position of X. citri pv. mangiferaeindicae XC01 and the red dotted line corresponds to the X. citri pv. mangiferaeindicae clade.Download as PowerPointTable 2. Repeat variable diresidues (RVDs) in transcription activator-like effectors (TALEs) of Xanthomonas citri pv. mangiferaeindicae strain GXG07GeneTALE classaRepeat variable diresidues (RVDs)StartbEndStrandChromosome tal1aTalILNI-NG-HD-NG-HD-HD-NG-NG-NG-NI-HD-HD-NG1,362,5181,365,503+ tal1bTalEDNI-NG-HD-NG-NI-NG-HD-NG-NG-HD-NI-NI-NG-HD-NI-NI-NI-NG1,368,5091,372,004+ tal2TalITNI-NG-HD-HD-NI-HD-NG-HD-NG-NG-HD-NG-NG-HD-NG-NI-NG-NG-HD-NG-NG1,385,9321,389,733+ tal3TalJANI-NG-NI-NI-NG-NG-HD-NI-NG-NI-NG-NI-NG-HD-NG1,401,1801,404,396− tal4aTalIUNI-NG-HD-NG-HD-NI-NI-HD-NI-HD-NG-NG-NG-HD-NI-NI-HD-NG1,829,3101,832,805+ tal4bTalIZNI-NG-NI-NG-HD-NI-HD-NI-HD-HD-HD-NI-NG-HD-NI-HD-NI-HD-HD-HD-HD-NI-HD-NG-NG1,836,6351,840,844− tal5TalIVNI-NG-NG-NG-HD-HD-NI-NG-HD-HD-NI-NG-HD-NI-NG-NG-NI-NI-NG-HD-NG-NG2,846,4862,850,389+pGXG07-1 tal6TalIWNI-NG-NI-NG-NI-NG-HD-NG-HD-NI-NG-NG-NG-NI-HD-HD-NG41,46444,856+ tal7TalIXNI-NS-NS-NI-NI-NS-HD-NS-NS-NG-NS-HD-NI-NI-NG-HD-NG-NG-HD-NI-NG52,47056,270+ tal8TalIYNI-NG-HD-HD-NG-HD-NG-HD-NG-NG-NG-NI-NI-NG-NG-HD-NG-NG61,37464,868+aTALE classes based on annoTALE (Grau et al. 2016).bGenomic coordinates of TALE genes in the genome of strain GXG07 (CP073209, CP073210, and CP073211).Table 2. Repeat variable diresidues (RVDs) in transcription activator-like effectors (TALEs) of Xanthomonas citri pv. mangiferaeindicae strain GXG07View as image HTML This whole-genome PacBio sequencing project has been deposited in NCBI under the accession numbers CP073209 (chromosome), CP073210 (pGXG07-1), and CP073211 (pGXG07-2).The author(s) declare no conflict of interest.Literature CitedAn, S. Q., Potnis, N., Dow, M., Vorhölter, F. J., He, Y. Q., Becker, A., Teper, D., Li, Y., Wang, N., Bleris, L., and Tang, J. L. 2020. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol. Rev. 44:1-32. https://doi.org/10.1093/femsre/fuz024 Crossref, ISI, Google ScholarCheng, H., Concepcion, G. T., Feng, X., Zhang, H., and Li, H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18:170-175. https://doi.org/10.1038/s41592-020-01056-5 Crossref, ISI, Google ScholarDoidge, E. M. 1915. 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Li contributed equally to this work.Funding: The work was supported by the National Key R&D Program of China (2018YFD0200302) and the Natural Science Foundation of China (31860033).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 106, No. 3 March 2022SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Downloaded 399 times Article History Issue Date: 30 Mar 2022Published: 8 Mar 2022First Look: 11 Oct 2021Accepted: 1 Oct 2021 Pages: 1027-1030 Information© 2022 The American Phytopathological SocietyFundingNational Key R&D Program of ChinaGrant/Award Number: 2018YFD0200302Natural Science Foundation of ChinaGrant/Award Number: 31860033Keywordsmango bacterial black spotXanthomonas citri pv. mangiferaeindicaePacBio sequencinggenome resourcetranscription activator-like effectorsThe author(s) declare no conflict of interest.PDF download