Complete genome sequencing of Xanthomonas citri pv. mangiferaeindicae XC01 in mango

Abstract:【Objective】Mango (Mangifera indica L.) , an evergreen plant that belongs to the Anacardiaceae family has been considered the“king of fruits”due to its nutritional value. The bacterial black spot of mango, also called mango bacterial canker, was observed in most mango cultivated countries and regions. It doesn't induce decline in infected trees, but leads to substantial crop losses, deteriorate fruit quality and decrease market value. Symptoms are observed as water soaked angular spots initially and then bacterial exudates deposit appeared on these necrotic portions lesions, which were clearly enclosed by some holes. Most aerial parts including mango fruits can be affected clearly by this pathogen. The unclearity of genomic sequences of X. citri pv. mangiferaeindicae is a major hindrance to understand the development and pathogenicity of this bacterium. In this study, the complete genome sequence of X.citri pv. mangiferaeindicae strain XC01 was studied, which was isolated from an infected mango fruit in Guangxi, China and the genes were highlighted with a demonstrated or proposed role in the pathogenesis.【Methods】The strain XC01, was isolated from an infected mango fruit in Guangxi, China. This bacterium was cultured aerobically in LB medium at 25 ℃. Genomic DNA from the strain XC01 was extracted using the UltraClean®Microbial DNA Isolation kit, and its quantity and quality were evaluatedon a NanoDrop spectrophotometer and a Qubit version 2.0 fluorometer. Complete genome of X. citri pv.mangiferaeindicae XC01 was sequenced by PacBio RS II high throughput sequencing platform. Then, fragment assembly, gene prediction, functional annotation, and GO/COG cluster were analyzed. To determine the position of the strain XC01 within the evolutionary precinct of Xanthomonas pathovars, the protein sequences of seven housekeeping genes were used, i.e, uvrY, secA, recA, groES, dnaK, gyrA and infB from 14 completely sequenced Xanthomonas spp..【Results】The deduced genome of X. citri pv.mangiferaeindicae strain XC01 was a circular chromosome of 3 856 165 bp. No plasmid was detected in the course of genome assembly. The average G+C content of strain XC01 genome was 68.9%. Gene prediction and annotation were performed by incorporating RNA-Seq data. A total of 3 442 protein-coding genes with an average length of 1 005 bp were predicted in the draft genome. Of the predicted genes, 3297 (95%) were assigned putative functions, and 145 (5%) had similarities to proteins of unknown function (conserved hypothetical proteins) . A total of 53 tRNAs representing 51 tRNA species were found on the genome using the tRNA scan-SE program. Two separate sets of 23 S-5 S and 16 S ribosomal RNA (rRNA) genes, each consisting of two operons were also identified. One defective prophage was found on the genome. The genome sequence of the XC01 was deposited at GenBank under the accession number CP016836. Out of 582 genes of the predicted strain XC01 genes, the highest proportion (46.39%) was attributed to the‘Reduced virulence'category, followed by a group of‘Unaffected pathogenicity' (15.12%) , Mixed outcome (10.31%) and Increased virulence (9.96%) as defined by the PHI database.The strain XC01 genome encodes 149 putative CAZymes including 45 glycoside hydrolases (GHs) , 30 glycosyl transferases (GTs) , 4 polysaccharide lyases (PLs) , 40 carbohydrate esterases (CEs) , 8 auxiliary activities (AAs) and 23 carbohydrate-binding modules (CBMs) . The highest numbers were observed for the carbohydrate esterases family 10 (CE-10) , carbohydrate-binding modules family 16 (CBM-16) and glycosyl transferases family 2. The phylogenetic tree indicates that X. citri pv. mangiferaeindicae strain XC01 is most closely related with X. citri pv. glycines CFBP 2526. The closest relative of X. citri pv.mangiferaeindicae strain XC01 is X. citri pv. glycines CFBP 2526, which causes bacterial pustule on soybeans.【Conclusion】In this study, we presented the whole genome sequence of strain XC01 and used that sequence to identify genes that might be involved in virulence. This study has also contributed to the available genomic resources for the study of the Xanthomonas bacterium.