Genome sequencing and comparative analysis of a new variant of Xanthomonas 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-VACAS J.; FILIPPONE M.P.; CASTAGNARO A.P., ; MARANO M.R.; ESTEBAN L.

Rosario

Congreso; IV Argentine Conference on Computational Biology and Bioinformatics and IV Conference of the Iberoamerican Society for Bioinformatics (SOIBIO); 2013

Society for Bioinformatics

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 [2] and Basys [3] for genome annotation. Manual curation of genes was performed with Artemis, a genome browser and annotation tool that allows visualization of sequence features. PanSeq [4] Novel Region Finder was used to detect unique fragments of both genomes. To asses Horizontal Gene Transfer (HGT) Island Viewer [5] was used because is a tool that integrates different genomic island prediction methods. Functional comparison was based on COG [6] and Rast assignments.