Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains

Additional File 1:

Codon bias relative to average gene versus third position GC content in eight variable regions of the Photobacterium profundum SS9 genome. In these graphs are represented only ORFs longer than 200 codons. Eight variable regions of the SS9 genome are considered, one for each graph. In red are highlighted ORFs located in regions that were found absent in 3TCK/DSJ4 genomes using comparative genomic hybridization experiments. A large number of ORFs are positioned in left and right horn of the graphs, a strong indication that they belong to laterally transferred regions.

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Additional File 2:

Detection of the 80 kbp plasmid in two different P. profundum strains. Comparison of strain TW30 (lanes A, B) with parental strain DB110 (lanes C, D) with plasmid specific primers. Lane E: no DNA control for PCR. Lane F: 2-log ladder marker (New England Biolabs).

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Additional File 3:

List of differentially expressed genes obtained in microarray experiments. This table reports only the ORFs identified univocally by the microarray clones and only those having log₂ ratio ≥|0.7| and "d score" obtained from SAM analysis = |2.3| (indicated with "1" in columns 7–12). Table columns report respectively: (1, 2, 3) ORFs differentially expressed in the three conditions under analysis, (4, 5) clones that were found absent in 3TCK and DSJ4 strains, (6) ORFs that were found absent in 3TCK strain ("3TCK"), in DSJ4 strain ("DSJ4") or in both strains ("3TCK-DSJ4"), (7) ORFs up-regulated at 28 MPa, (8) ORFs down-regulated at 28 MPa, (9) ORFs up-regulated at 4°C, (10) ORFs down-regulated at 4°C, (11) ORFs up-regulated at 45 MPa, (12) ORFs down-regulated at 45 MPa, (13) ORF annotation, (14) spotted microarray clones identifying each ORF, (15, 16), (17, 18), (19, 20) ("log₂ ratio" and "d value") mean value of expression differences calculated as log₂ [(Σ fluorescence value at 28 MPa)/(Σ fluorescence value at 0.1 MPa)] and the "d" statistic value obtained from SAM analysis. Each ORF is identified by one or more clones and not all ORFs identified from each clone are reported in the table (for a complete picture see the UCSC genome browser [12]). Row data obtained from microarray experiments were submitted to ArrayExpress database at EBI with accession numbers E-MEXP-210, E-MEXP-348, E-MEXP-374, E-MEXP-375, E-MEXP-376.

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Additional File 4:

List of ORFs absent only in 3TCK strain. Data obtained from genomic comparison experiments between 3TCK (the pressure sensitive strain) and SS9 strain. In this table are reported ORFs that were found absent only in 3TCK and not in DSJ4 strain. In order to obtain a more reliable result, clones obtained from SAM analysis of 3TCK strain were filtered considering only those having log₂ ratio higher than +1 and d statistic value higher than +1.8. Using self-written PERL scripts, from the "3TCK clones" set, were subtracted the clones that were found absent also in DSJ4. In DSJ4 strain we used less stringent criteria and we considered all clones having log₂ ratio higher than 0.5. Clones absent both in 3TCK and DSJ4 were discarded. Clones absent only in 3TCK were associated with ORFs position and the list of ORFs obtained were manually verified. Table columns show: (1) the locus name, (2) the ORF description, (3) the TrEMBL code, (4) the microarray clone/s overlapped to the ORFs, (5) the log₂ ratio obtain from comparison with SS9 genome (reference), (6) the "d" statistic value obtained from SAM analysis and (7) the result obtained in microarray expression experiments. In the first column large groups of ORFs that are adjacent in the SS9 genome are highlighted using bold character.

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Additional File 5:

List of Gene Ontology categories of differentially expressed genes. In this table differentially expressed genes reported in Additional file 3 are categorized in Gene Ontology classes using GoMiner software. Only highly significant GO classes are reported. Table columns show: (1) the Gene Ontology ID, (2) the total number of P. profundum SS9 genes belonging to each class, (3, 4, 5) the "p statistic value" of down-regulated, up-regulated and differentially expressed genes, (6) the Gene Ontology term, (7) the "UniProtKB/TrEMBL" primary accession number, (8) the ordered locus name, (9) the name of differentially expressed genes belonging to each Gene Ontology category and (10) their "up-" or "down-regulation".

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