Journal of Microbial & Biochemical Technology

Comparative genomics of subspecies of pantoea stewartii

2^nd International Conference on Clinical Microbiology & Microbial Genomics

September 16-17, 2013 Hampton Inn Tropicana, Las Vegas, NV, USA

Zaky Adam

Posters: J Microb Biochem Technol

Abstract:

Plant-associated Pantoea are either epiphytes or pathogens and constitute the majority of validly described species of this genus. Pantoea stewartii includes two subspecies ( stewartii and indologenes ) delineated based on indole production. However, a multi-locus sequence analysis using six housekeeping genes identified two strains (DOAB 230 and DOAB 231), classified as Pantoea stewartii ssp. indologenes based on indole production, which clustered distinctively from the type strain LMG 2632. The objective of this work was to use comparative genomics to understand better the delineation of subspecies of Pantoea stewartii . The genomes of DOAB 21 (subspecies stewartii ), DOAB 213 (subspecies indologenes ) and DOAB 230 (subspecies nov.) were sequenced using Illumina HiSeq technology. De novo assembly was performed because there is no publicly available genome of Pantoea stewartii . DOAB 213 sequencing utilized 150 bp paired-end reads with 360 bp inserts. DOAB 230 and DOAB 21 sequencing utilized 101 bp paired-end reads with 300 bp inserts. The genomes were optimally assembled based on various k-mer values and using multiple assemblers including Velvet and Abyss. The resulting scaffolds were produced using SSPACE, and gaps between contigs within scaffolds were filled using GapFiller. All the draft genomes assembled in this study showed highest similarity with P. ananatis LMG 5342. Percentage similarities between Pantoea ananatis LMG 5342 and DOAB 213 (73%) or DOAB 21 (76%) were comparable, while strain DOAB 230 (87%) showed the highest similarity. Using Glimmer, the number of genes predicted in P. stewartii ssp. Indologenes DOAB 213, P. stewartii ssp. stewartii DOAB 21, and P. stewartii ssp. nov. DOAB 230 were 5396, 6129, and 4727 respectively. These genome sequences will provide a better delineation of subspecies of P. stewartii