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GC-Rich Genome of Pandoraea Bacterium Assembled with SMRT Sequencing

Tuesday, April 8, 2014

Scientists from the Institute of Biological Sciences at the University of Malaya recently published a description of Pandoraea sp. strain RB-44 in Genome Announcements, a journal from the American Society for Microbiology. The genome sequence was completed using Single Molecule, Real-Time (SMRT®) Sequencing.

Pandoraea is a soil bacterium; this particular strain was collected from the site of a former landfill. Some strains of Pandoraea have been suggested as cystic fibrosis clinical pathogens, the authors report, though “their role in pathogenicity is still largely unknown.”

Corresponding author Kok-Gan Chan and colleagues may have a new lead in that mystery. Their Pandoraea strain is the first one found to conduct quorum sensing, “a communication mechanism that is known to mediate cell-to-cell interaction between proteobacteria,” the scientists report. “Various essential bacterial activities are coordinated by this mechanism, for instance, virulence, formation of biofilms, antibiotic synthesis, motility, and swarming activities.”

To generate the genome sequence, the scientists used the PacBio® RS II platform with P4 chemistry and a 10 Kb SMRTbell™ library. Sequencing was completed on four SMRT Cells, resulting in an average of nearly 150x coverage for the genome. Assembly using HGAP yielded a single contig of 5.3 Mb with 64.9% GC content. Further analysis was used to detect 69 tRNA genes and 12 rRNA operons in the organism’s genome. “To the best of our knowledge, this is the first documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea species,” the authors note.

Find out more about the benefits of generating complete microbial genomes at the American Society for Microbiology (ASM) annual meeting in May (Booth #1034). 

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