Complete Genome Sequence of Xanthomonas phaseoli pv. manihotis Strain CHN01, the Causal Agent of Cassava Bacterial Blight

HomePlant DiseaseVol. 106, No. 3Complete Genome Sequence of Xanthomonas phaseoli pv. manihotis Strain CHN01, the Causal Agent of Cassava Bacterial Blight PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseComplete Genome Sequence of Xanthomonas phaseoli pv. manihotis Strain CHN01, the Causal Agent of Cassava Bacterial BlightShousong Zhu, Yueyun Pan, Ke Li, Ruochen Fan, Li Xiang, Siyuan Huang, Suhang Jia, Xiaolei Niu, Chunxia Li, and Yinhua ChenShousong ZhuHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author, Yueyun PanHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaJiaxing Academy of Agricultural Science, Jiaxing 314016, Zhejiang, ChinaSearch for more papers by this author, Ke LiHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author, Ruochen FanHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author, Li XiangHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author, Siyuan HuangHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author, Suhang JiaHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author, Xiaolei NiuHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author, Chunxia Li†Corresponding authors: C. X. Li; E-mail Address: chun_xia_li@126.com, and Y. H. Chen; E-mail Address: yhchen@hainanu.edu.cnHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author, and Yinhua Chen†Corresponding authors: C. X. Li; E-mail Address: chun_xia_li@126.com, and Y. H. Chen; E-mail Address: yhchen@hainanu.edu.cnhttps://orcid.org/0000-0002-9232-7590College of Life Science, Hainan University, Haikou 570228, Hainan, ChinaSearch for more papers by this author AffiliationsAuthors and Affiliations Shousong Zhu1 Yueyun Pan1 2 Ke Li1 Ruochen Fan1 Li Xiang1 Siyuan Huang1 Suhang Jia1 Xiaolei Niu1 Chunxia Li1 † Yinhua Chen3 † 1Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China 2Jiaxing Academy of Agricultural Science, Jiaxing 314016, Zhejiang, China 3College of Life Science, Hainan University, Haikou 570228, Hainan, China Published Online:8 Mar 2022https://doi.org/10.1094/PDIS-09-21-2016-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementXanthomonas phaseoli pv. manihotis (Xpm) is the causative agent of bacterial blight on cassava (Manihot esculenta Crantz), one of the most devastating diseases threatening worldwide cassava production. Currently, genome sequences for only a few Xpm isolates are available from China. Here, we assembled a complete and closed genome sequence of a cassava-pathogenic X. phaseoli pv. manihotis isolate Xpm CHN01 via PacBio single-molecule real-time (SMRT) sequencing, which comprises about 4.79 Mb circular chromosome and four plasmids. The genomic data presented in this study enrich the current Xpm genome database, extend our comprehension to the Xpm genomic features, and pave the way for research on functional and interaction genetics to combat the risk of cassava bacterial blight.Xpm generates yield losses ranging from 12 to 100% (Lozano 1986; Mansfield et al. 2012). It is a foliar and vascular pathogenic bacterium that can induce a wide range of unique symptoms among disease caused by plant pathogenic bacteria, including angular leaf spots, wilting, blighting, vascular necrosis of the stem, dieback, and gum exudates (Verdier et al. 1998).Cassava bacterial blight (CBB) was first reported in Brazil in 1912. Since then, it has been found and identified in almost all countries of Asia, Africa, and Latin America where cassava is cultivated (Elango and Lozano 1980). To date, Xpm has been reported in 49 countries located all over the tropics (Zárate-Chaves et al. 2021). Xpm has been reported to symptomatically infect five Euphorbiaceous plants: three cassava wild relative species Manihot glaziovii, Manihot palmate, and Manihot aipi (Lozano and Sequeira 1974), Euphorbia pulcherrima, and Pedilanthus tithymaloides (Dedal et al. 1980).Open wounds and stomata are major routes of Xpm infection in otherwise healthy cassava plants (Lozano and Sequeira 1974). The exchange of contaminated cassava stem cuttings has contributed to the migration of Xpm and, consequently, has influenced the genetic structure of its populations (Restrepo et al. 2000). Currently, Xpm is considered as a quarantine pathogen in all countries that grow cassava. Using resistant cassava varieties or pathogen-free cuttings is still the most effective way to control CBB (Mansfield et al. 2012). Cassava disease resistance also needs further research and is permanently challenged by the diversity of Xpm strains (Jorge et al. 2000; Zárate-Chaves et al. 2021).The type III-secreted effector proteins (T3Es) play an important role in pathogenicity. Recently, several research projects have reported the genomic sequence and pathogenicity genes in Xpm (Arrieta-Ortiz et al. 2013; Bart et al. 2012). Up to now, many T3Es have been identified in the plant pathogen of the genus Xanthomonas, while only a few of T3Es have been reported in Xpm (Castiblanco et al. 2013; Cohn et al. 2016; Medina et al. 2018). In particular, Xanthomonas out proteins (Xops) were barely reported. Besides, there are almost no genome sequence reports about Xpm in China. Additional high-quality complete genome sequences for various Xpm isolates will contribute to our knowledge of Xpm genomic diversity. It is urgent to better understand the pathogenicity determinants of Xpm for efficiently controlling CBB.Xpm strain CHN01 was isolated from cassava leaves showing CBB-like symptoms in Hainan Province, China, in 2017, and identified according to a previous study (Abdulai et al. 2018). The total genomic DNA of CHN01 was extracted using TIANamp Bacteria DNA kit (TIANGEN, China) following the manufacturer’s instructions. Approximately 10 kb genomic fragments were prepared using Covaris g-TUBE (Thermo Fisher Scientific, U.S.A.). Then, the 10-kb SMRT Bell library was constructed and sequenced using long-read SMRT sequencing via PacBio RSII platform (Pacific Biosciences, U.S.A.). A total of 706,993,902 filtered polymerase read bases were obtained by filtering out reads with quality less than 0.75, removing adapters with self-linkers, and short polymerase reads (<50 bp) via SMRT analysis package (v2.3.0) (Pacific Biosciences, U.S.A.). The genome assembly was conducted using Canu (v1.5), including self-correction, trimming, and assembly (Koren et al. 2017). The final assembly was confirmed by Pilon (v1.18) (Walker et al. 2014), and the annotation were done with Glimmer (v3.0.1) (Delcher et al. 1999). The total assembly length of Xpm CHN01 was 5,200,720 bp (approximately 136× coverage) with no gaps, and 64.9% of the G+C content, which is similar to other Xpm strain genomes (Arrieta-Ortiz et al. 2013; Bart et al. 2012). It contains a single circular chromosome of 5,021,664 bp with G+C content of 65.05%, along with four circular plasmids, pXPM48 (48,702 bp), pXPM45 (45,604 bp), pXPM44 (45,336 bp), and pXPM38 (39,414 bp). The N50 and L50 are 5,021,664 and 5, respectively. A total of 4,958 genes were identified, and 55 tRNA genes and 6 rRNA genes were predicted using tRNAscan-SE (v1.3.1) (Lowe and Eddy 1997) and Barrnap (v0.8). The average gene length was 911.21 bp and about 85.82% of the CHN01 genome was covered in genes. Gene functional annotation analysis showed that approximately 4,898 (98.79%), 3,152 (63.57%), 3,655 (73.72%), 3,850 (77.65%), 3,303 (66.62%), and 2,327 (46.93%) genes were annotated from the National Center for Biotechnology Information Non-Redundant (NCBI-NR) database, Swiss-Prot, Protein Families (Pfam) database, Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, respectively. A comparative account on genomic features of Xpm CHN01 with other previously reported Xpm strains, including Indonesia strain Xpm 668 and Colombia strain Xpm CIO151, was determined (Table 1). Compared with these two Xpm genomes, Xpm CHN01 was predicted to have more coding sequences, with approximately 97.44% or 86.11% fewer contigs/scaffolds (5 versus 195 or 36) and a 109- or 12-fold higher contig/scaffold N50 (5,021,664 bp versus 46,240 bp or 429,565 bp).Table 1. Comparative accounts on genomic features of Xpm CHN01 with other Xpm strainsGenomic featuresChina Xpm CHN01Indonesia Xpm 668Colombia Xpm CIO151Length (bp)5,200,7204,954,8605,150,175Number of contigs or scaffolds519536G + C content (%)64.964.964.0Predicted coding sequence (CDS)4,8984,0834,109Contig or scaffold N505,021,66446,240429,565Contig or scaffold L505295tRNAs554954rRNAs635Plasmids405ReferenceThis studyBart et al. (2012)Arrieta-Ortiz et al. (2013)Table 1. Comparative accounts on genomic features of Xpm CHN01 with other Xpm strainsView as image HTML Here, we describe the first complete genome sequence of Xpm strains isolated from China to provide a representative genome for further comparative analyses with the available sequenced Xpm stains deposited online. The Xpm CHN01 genomic data presented in this study will contribute to our comprehension of Xpm genomic variation, Xpm evolution in China, Xpm-cassava interactions, and will be helpful for developing new strategies to prevent and control CBB. Much remains to be performed to improve our ability to combat this economically important plant disease.Data AvailabilityThe complete genomic data of Chinese Xpm strain CHN01 have been deposited to the NCBI GenBank database under the accession nos. CP083575, CP083576 (pXPM38), CP083577 (pXPM44), CP083578 (pXPM45), and CP083579 (pXPM48).AcknowledgmentsWe thank Dr. Zhiqiang Xia at the College of Tropical Crops, Hainan University for his support to our genome projects. We also thank Prof. Xiaofei Zhang from Alliance of Bioversity International and CIAT for his revised recommendation.The author(s) declare no conflict of interest.Literature CitedAbdulai, M., Basım, H., Basım, E., Baki, D., and Öztürk, N. 2018. 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Pan contributed to this work equally.Funding: This research was supported by the National Key Research and Development Program of China (2018YFD1000500) and China Agriculture Research System (CARS-11-HNCYH).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 106, No. 3 March 2022SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Downloaded 467 times Article History Issue Date: 30 Mar 2022Published: 8 Mar 2022Accepted: 23 Nov 2021 Pages: 1039-1041 Information© 2022 The American Phytopathological SocietyFundingNational Key Research and Development Program of ChinaGrant/Award Number: 2018YFD1000500China Agriculture Research SystemGrant/Award Number: CARS-11-HNCYHKeywordscassava bacterial blightXanthomonas phaseoli pv. manihotisgenomepathogen detectionyield loss and economic impactsThe author(s) declare no conflict of interest.PDF download