Solexa pair end sequencing technology

DNA was prepared from 1 ml of cultures grown overnight with a Wizard genomic DNA purification kit (Promega) according to the manufacturer’s instructions. The genomic sequencing was performed using Solexa pair-end sequencing technology (Illumina, Little Chesterford, Essex, United Kingdom), with a depth of 90-fold to 100-fold coverage. The reads were subjected to de novo assembly using VelvetOptimiser v2.2 (47 (link)). The annotation of newly sequenced genomes was performed using the NCBI Prokaryotic Genome Annotation Pipeline (https://www.ncbi.nlm.nih.gov/genome/annotation_prok).

Genome sequencing of PCM1220 was performed using Pac Bio RS II (Pacific Biosciences).
The other 20 strains were sequenced using Solexa pair-end sequencing technology
(Illumina, Little Chesterford, Essex).
For PCM1220, a 20-kb library was constructed and end-repaired, and the adaptors were
then ligated to generate Single Molecule Real Time (SMRT) bells™ for circular
consensus sequencing, with a depth of approximately 100-fold coverage. The sequencing
data were de novo assembled using MaSuRCA [22 (link), 23 (link)].
A Solexa Genome Analyzer IIx was used to sequence each isolate with a depth of 90- to
100-fold coverage. The Illumina data were de novo assembled using
Velvet Optimiser v2.2 (http://bioinformatics.net.au/software.velvetoptimiser.shtml) [22 (link)]. Gaps within the gene
clusters containing the major polysaccharide antigens were closed using PCR, and the
products were then sequenced using ABI 3730 capillary sequencers (Applied Biosystems,
U.S.A).

The genomic sequencing performed using Solexa pair-end sequencing technology (Illumina, Little Chesterford, Essex), with a depth of 90–100-fold coverage. The reads were de novo assembled using Velvet Optimiser v2.2 (Zerbino and Birney, 2008 (link)). The assembly statistics for all newly sequenced Providencia genomes were showed in Supplementary Table S1. The annotation of newly sequenced genomes was performed by NCBI Prokaryotic Genome Annotation Pipeline¹. All genomes data in our research were accessed by CheckM (Parks et al., 2015 (link)), and related statistics were showed in Supplementary Table S1.