Caulobacter vibrioides NA1000
Library preparation and sequencing protocol: Genomic DNA (gDNA) was extracted using a ChargeSwitch Kit_ (Thermo Fisher Scientific) following the manufacturerÕs protocol. After elution, gDNA quality and concentration was assessed by measurement of the A260/A280 and A260/A230 ratios with a Nanodrop device (Thermo Fisher Scientific) and ethidium bromide staining in agarose gel. gDNA integrity and size was evaluated by running an Agilent Bioanalyzer gel prior to library preparation. Library preparation and sequencing was performed by the Yale Center for Genome Analysis as follows: ~500ng of gDNA with size 10-20 Kb was sheared using a Covaris E210 (Covaris, Woburn, MA) and further purified using Ampure XP SPRI beads (Beckman Coulter Genomics). The DNA was then end-repaired, A-tailed, adapter ligated and PCR enriched (5 cycles). Indexed libraries were that met appropriate cut-offs  were quantified by both  qRT-PCR  and insert size distribution was determined with the LabChip GX (Perkin Elmer, Waltham, MA). Samples with a yield of ³0.5 ng/µl were used for sequencing. Subsequently, sample concentrations were normalized to 2 nM and loaded into High-output flow cells (Illumina, San Diego CA) at a concentration that yields ~200 million passing filter clusters per lane. Samples were sequenced using 75 bp paired-end sequencing on an Illumina HiSeq 2500 according to Illumina protocols. The 6 bp index was read during an additional sequencing read that automatically followed the completion of read 1. A positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time. Reads obtained from sequencing were trimmed and aligned to the C. crescentus NA1000 reference genome CP001340.1 using the Bowtie software (Li and Durbin, 2009). Downstream analysis was done with MATLAB software.