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Article

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald

1
National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
2
CIRAD, UMR BGPI, F-34398 Montpellier, France, and BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, F-34398 Montpellier, France
3
School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Microorganisms 2020, 8(2), 182; https://doi.org/10.3390/microorganisms8020182
Received: 28 December 2019 / Revised: 22 January 2020 / Accepted: 24 January 2020 / Published: 28 January 2020
(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))
Leaf scald (caused by Xanthomonas albilineans) is an important bacterial disease affecting sugarcane in most sugarcane growing countries, including China. High genetic diversity exists among strains of X. albilineans from diverse geographic regions. To highlight the genomic features associated with X. albilineans from China, we sequenced the complete genome of a representative strain (Xa-FJ1) of this pathogen using the PacBio and Illumina platforms. The complete genome of strain Xa-FJ1 consists of a circular chromosome of 3,724,581 bp and a plasmid of 31,536 bp. Average nucleotide identity analysis revealed that Xa-FJ1 was closest to five strains from the French West Indies and the USA, particularly to the strain GPE PC73 from Guadeloupe. Comparative genomic analysis between Xa-FJ1 and GPE PC73 revealed prophage integration, homologous recombination, transposable elements, and a clustered regulatory interspaced short palindromic repeats (CRISPR) system that were linked with 16 insertions/deletions (InDels). Ten and 82 specific genes were found in Xa-FJ1 and GPE PC73, respectively, and some of these genes were subjected to phage-related proteins, zona occludens toxin, and DNA methyltransferases. Our findings highlight intra-species genetic variability of the leaf scald pathogen and provide additional genomic resources to investigate its fitness and virulence. View Full-Text
Keywords: bacterial disease; Xanthomonas albilineans; average nucleotide identity (ANI); structural variation; specific genes bacterial disease; Xanthomonas albilineans; average nucleotide identity (ANI); structural variation; specific genes
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MDPI and ACS Style

Zhang, H.-L.; Ntambo, M.S.; Rott, P.C.; Chen, G.; Chen, L.-L.; Huang, M.-T.; Gao, S.-J. Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald. Microorganisms 2020, 8, 182. https://doi.org/10.3390/microorganisms8020182

AMA Style

Zhang H-L, Ntambo MS, Rott PC, Chen G, Chen L-L, Huang M-T, Gao S-J. Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald. Microorganisms. 2020; 8(2):182. https://doi.org/10.3390/microorganisms8020182

Chicago/Turabian Style

Zhang, Hui-Li, Mbuya Sylvain Ntambo, Philippe C. Rott, Gongyou Chen, Li-Lan Chen, Mei-Ting Huang, and San-Ji Gao. 2020. "Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald" Microorganisms 8, no. 2: 182. https://doi.org/10.3390/microorganisms8020182

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