Computational protocol: Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin

Similar protocols

Protocol publication

[…] The genomes of L. casei strains LcA and LcY were sequenced using two next-generation sequencing platforms (454 GS-FLX+, Life Sciences and SOLiD, Life Technologies) and assembled de novo at the Institute of Biotechnology (Helsinki, Finland). The combination of both platforms allowed a much greater sequencing depth and accuracy in contrast to a unique sequencing technology approach, as previously done for L. casei strains LcA and LcY (Douillard et al., ). The 454 coverage on basis of numbers of reads in contigs is averaging 14X for both LcA and LcY genomes and the SOLiD coverage estimated from mappings is of ∼88X for LcA and ∼107X for LcY. Using progressive Mauve genome alignment package (Darling et al., ), the draft contigs were ordered and oriented. The published genomes of L. casei BL23, W56, BD-II and LC2W were used as references, improving the draft genome assemblies. Automatic genome annotation was conducted using RAST pipelines (Aziz et al., ) and subsequently RATT (Otto et al., ). PCR amplification from total DNA was performed to confirm contig order and circularity of the plasmids identified in both L. casei strains LcA and LcY. Pseudogenes and transposases were not addressed in the present study. Signal sequences were predicted with SignalP v4.0 (Petersen et al., ) and LPxTG proteins were identified using CW-PRED (Litou et al., ). BLAST Ring maps were generated using BRIG (Alikhan et al., ). SNPs and InDels analysis of both draft genomes was performed as follows. The LcA SOLiD reads were mapped to the LcY draft genome sequence using SHRiMP2, and BAM files of the mapping result were generated using SAMtools (Li et al., ; Rumble et al., ). Similarly, the LcY SOLiD reads were mapped to the LcA draft genome sequence. SNPs and InDels were detected with the MUMmer software package using nucmer parameters ‘maxmatch’ and ‘-c 100’, and show-snps command was used with parameter ‘-C’ (Kurtz et al., ). Only unequivocal SNPs and InDels detected in both mappings were reported. Read mappings and annotations were inspected with Artemis (Carver et al., ). […]

Pipeline specifications

Software tools Mauve, RAST, RATT, SignalP, BRIG, SHRiMP, SAMtools, MUMmer, Artemis
Applications Nucleotide sequence alignment, Genome data visualization
Organisms Lactobacillus casei, Homo sapiens
Chemicals Lactose