johnsonii genome In silico genome-wide screen of L. johnsonii NCC 533 revealed thousands of SSR tracts that were evenly distributed Selleckchem AZD8931 and highly abundant along the genome Eleven loci with the largest number of repeats were chosen for genetic characterization of L. johnsonii (Table 2), having motif sizes ranging from

1 to 480 bp. Ten SSR loci were located in coding regions and one mononucleotide repeat (MNR) locus was located in a noncoding region. Multiple alleles were found at the studied SSR loci among 47 isolates from various hosts, including eight additional strains mainly from humans (generous gift from Nestle Company, Table 1), revealing a high level of polymorphism among L. johnsonii strains (Table 2). Two strategies were used Dinaciclib molecular weight to identify the polymorphism: sizing for the SSR loci, and sequencing for the MNR locus. Most SSR loci did not amplify any product (a null allele) in some of the isolates (Table 2). Variation at the MNR locus was observed only in the repeated tract, while the flanking sequences were conserved among isolates. All SSR loci presented 2 to 10 alleles with corresponding diversity indices ranging from 0.28 to 0.76. Table 2 Number of alleles and diversity index values at the studied 14 loci among  L. johnsonii  isolates Locus Core motif size (bp) and no. of repeatsa,b Gene product No. of alleles or STc,d Diversity index SSR

loci         LJ480 (480)3 Hypothetical protein 5 0.47 LJ90 (90)9 Hypothetical protein 7 0.56 LJ66 (66)7 Hypothetical protein 5 0.50 LJ27 (27)6 Hypothetical protein 10 0.76 LJ18 (18)3 Hypothetical protein 2 0.28 LJ12 (12)4 Signal recognition particle receptor FtsY 7 0.72 LJ9 (9)3 Phosphoenolpyruvate-dependent sugar phosphotransferase system EIIC 3 0.66 LJ6 (6)7 Putative tyrosine-protein kinase 6 0.74 LJ6_1 (6)3 Cell-wall associated serine Danusertib order proteinase 3 0.29 LJ3 (3)5 Hypothetical Thalidomide protein 4 0.64 LJ_mono (1)11 Noncoding 5 0.44 MLST Sequence lengthb (bp)     LJ0017e 1113 ‘Conserved hypothetical’ gene 23   LJ0648 522 ‘Conserved hypothetical’ gene 24   LJ1632 286 ‘Conserved hypothetical’ gene 10   a Subscript numbers are numbers of motif repeats. SSR loci have

non-perfect repeats except for loci LJ3 and LJ_mono. b Based on the genome sequence of L. johnsonii NCC 533. c Allele: number of repeat variant at SSR; ST: number of sequence types at ‘Conserved hypothetical’ genes. d No. of alleles or ST: MLST genes and SSR loci, except for the locus LJ3, included a null allele. e Isolates: LJ_352, LJ_353, LJ_363, LJ_365, LJ_ch1, LJ_c2-8, LJ_c5-1, LJc_3-4 and LJ_c6-5 had a deletion of 903 bp. Sequence variation at conserved hypothetical genes Three conserved hypothetical genes were chosen for MLST (Table 2). Most isolates gave the expected product size, except for nine isolates which had a deletion of 903 bp in the LJ0017 gene. The Psammomys isolate (LJ_56) did not amplify any product in any of the genes. Sequence variation among isolates was rather high (12.