Genome Sequencing and Annotation of Bacterial Strains

Genome Analyzer IIx of the Illumina-Solexa platform at the Biomedical Genomics Research Center of Korea Research Institute of Bioscience and Biotechnology was used for genome sequencing. 22,525,438 high-quality reads with 233-fold coverage for NCCP15655 and 27,858,714 high-quality reads with 235-fold coverage for NCCP15656 were generated from 500-bp paired-end libraries. Sequence trimming and de novo assembly were performed using CLC Genomics Workbench version 5.1 (CLC bio, Inc.) and scaffolding was carried out with SSPACE [17 (link)]. Automatic gap filling was performed using IMAGE [18 (link)] and manual gap filling was performed using CLC Genomics Workbench. Structural gene prediction was performed using Glimmer 3 [19 (link)] and functional annotation was performed using blastp against MicroScope database [20 (link)] of E. coli and Shigella species. We then employed automatic annotation using the RAST server [21 (link)] and compared it with the annotation result from MicroScope database for more accurate functional assignment. We also performed additional blastp against the subsystem database of the RAST server for the gene categorization.