Genome atlas view of the scaffolded contigs of <i>L. pentosus</i> KCA1.

<p>From the outer circle inward: The first ring shows the entire chromosome. The second ring shows the location of the 83 contigs based on <i>L. plantarum</i> WCFS1 genome order/orientation as template. The black arrow-heads indicates the position of some of the genes of interest located in the corresponding contigs described in the text with the locus tag in bracket. The fourth ring shows the local %GC plot and the innermost circle shows the GC-skew with sharp changes occurring at the origin and terminus of replication. The Atlas was constructed using DNA plotter.</p

Phylogenetic tree of <i>Lactobacillus</i> species showing the position of <i>L. pentosus</i> KCA1 based on the 16S rRNA gene sequences.

<p>The numbers at the end of each strain indicates the accession number. Sequences were aligned with MUSCLE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059239#pone.0059239-Finn1" target="_blank">[58]</a>, and unreliable positions were curated using Gblocks <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059239#pone.0059239-Edgar1" target="_blank">[59]</a>. A maximum likelihood tree was generated by PhyML using the GTR substitution model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059239#pone.0059239-Castresana1" target="_blank">[60]</a> and allowing 4 rate substitution categories. Confidence values for the branching order were generated by bootstrapping (based on 100 replications). The number at the nodes indicates the bootstrap values. The scale bar indicates 1 nucleotide substitution per 100 nucleotides.</p

Summary of housekeeping genes sequence identity matrices (%) to pentosus and plantarum strains.

<p>ND = Not Done.</p

Phylogenetic tree of Lactobacillus species showing the position of <i>L. pentosus</i> KCA1 based on the sequences of the housekeeping gene recA, relative to other plantarum and pentosus strains.

<p>The numbers at the end of each strain indicates the accession number. Sequences were aligned with MUSCLE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059239#pone.0059239-Finn1" target="_blank">[58]</a>, and unreliable positions were curated using Gblocks <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059239#pone.0059239-Edgar1" target="_blank">[59]</a>. A maximum likelihood tree was generated by PhyML using the GTR substitution model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059239#pone.0059239-Castresana1" target="_blank">[60]</a> and allowing 4 rate substitution categories. Confidence values (%) for the branching order were generated by bootstrapping (based on 100 replications). The number at the nodes indicated the bootstrap values. The scale bar indicates 1 nucloetide substitution per 100 nucleotides.</p

Whole genome alignment of <i>L. pentosus</i> KCA1 with <i>L. pentosus</i> IG1.

<p>Constructed with the ACT tool. Red lines indicate orthologous genes in the same orientation. Blue lines indicate orthologous genes in reverse orientation. The large inverted region in <i>L. pentosus</i> IG1 is indicated.</p

Class V bacteriocin biosynthesis gene cassettes and their organization in three <i>Lactobacillus</i> species including <i>L. pentosus</i> KCA1.

<p>PenA represents the pentocin KCA1 precursor. Adapted from Kawai et al, 2009, AEM 75∶1324–1330.</p

Toxin-antitoxin systems predicted in L. pentosus KCA1.

<p>Toxin-antitoxin systems predicted in L. pentosus KCA1.</p

Comparison of sequenced genomes of L. pentosus, L. plantarum and L. iners strains.

<p>Comparison of sequenced genomes of L. pentosus, L. plantarum and L. iners strains.</p

Phage resistance via abortive infection proteins predicted in L. pentosus KCA1.

<p>Phage resistance via abortive infection proteins predicted in L. pentosus KCA1.</p