Genome sequencing and comparative analysis of a new variant ofXanthomonas citri subsp. citri that triggers a host-specific defense response in Citrus limon.

CABRAL, J; FAVARO, M.A; DANDREA, R.M; CHIESA, M.A; ROESCHLIN, R.A; GADEA, J.; FILIPPONE, M.P.; CASTAGNARO, A.P; MARANO, M.R; ESTEBAN, L

Rosario

Congreso; . 4to Congreso Argentino de BioInformática y Biología Computacional y 4ta. Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SoIBio); 2013

Citrus is an economically important fruit crop that is severely afflicted by Asiatic citrus bacterial canker, a disease caused by the phytopathogen Xanthomonas citri subsp. citri (X. citri). Recently, we have characterized a new variant of X. citri, named X. citri AT, which induces an atypical, non-cankerous chlorotic phenotype in Citrus limon and C. paradisi and weak cankerous lesions in C. aurantifolia and C. clementina leaves [1]. We used high-throughput sequencing to determine the genome sequence of isolate AT of X. citri. The short reads were de novo assembled and the resulting contigs were ordered using a reference genome sequence from the strain X. citri 306 that induces canker disease. To accomplish a full genomic comparison between these two sequences we used different bioinformatics tools, including Rast (Rapid Annotation using Subsystem Technology) and Basys (Bacterial Annotation System) for genome annotation. Manual curation of genes was performed with Artemis, a genome browser and annotation tool that allows visualization of sequence features. PanSeq Novel Region Finder was used to detect unique fragments of both genomes. To asses Horizontal Gene Transfer (HGT) Island Viewer was used because is a tool that integrates different genomic island prediction methods. Functional comparison was based on COG (Clusters of Orthologous Groups) and Rast assignments.