lactis IL1403/Streptococcus pneumoniae TIGR4 b ++ Genes detected in both alignments, L. lactis subsp. lactis IL1403 array probes vs S. pneumoniae TIGR4 genome, and S. pneumoniae TIGR4 array probes vs L. lactis subsp. lactis IL1403
genome; + positive in one of the two cases. c Only the results for the negative genes in BLAT80 are shown. d Only the results for the negative genes in both ZD1839 datasheet BLAT80 and BLAT70 are shown. After combined analysis of the results obtained in silico and in vitro, we established, under the hybridization conditions Selleckchem PR-171 used in this study, a detection threshold based on a sequence similarity of ≥ 70% for alignments longer than 100 bp. This was established as the reference framework for the inter-species CGH assays. In vitro microarray CGH experiments with L. garvieae CECT 4531 vs reference microorganisms L. lactis subsp. lactis IL1403 and S. pneumoniae TIGR4, and in silico analysis of available
sequences from L. garvieae The microarray CGH experiments selleck inhibitor identified 267 genes in L. garvieae that had analogues in L. lactis from and/or S. pneumoniae (Additional file 1). Of these, 111 genes (41.6%) were identified only with the L. lactis microarray, 70 genes (26.2%) only with the microarray of S. pneumoniae, and 86 genes (32.2%) were identified with both microarrays. These genes belong to diverse functional groups (Table 2). Most of the genes (96.6%) have been documented for the first time in L. garvieae.
Only nine genes (four present in both reference microorganisms: atpD/SP1508, pfk/SP0896, tig/SP0400, tuf/SP1489; three present in L. lactis: als, ddl, galK; two present in S. pneumoniae: SP0766, SP1219) out of the 267 genes detected have been either identified or sequenced before in diverse strains of L. garvieae (Tables 3 and 4). In silico analysis of these previously sequenced genes (n = 9) of L. garvieae were performed to assess the efficacy of the methodology. Alignments of these available sequences with the genomes of the corresponding reference microorganism and their respective array probes showed nucleotide identities ranging between 70% and 86% (Tables 3 and 4).