Open Access Highly Accessed Research article

Legionella pneumophila pangenome reveals strain-specific virulence factors

Giuseppe D'Auria12*, Nuria Jiménez-Hernández12, Francesc Peris-Bondia3, Andrés Moya123 and Amparo Latorre123

Author Affiliations

1 CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain

2 Area de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), (Avda. de Cataluña, 21), Valencia, (46020), Spain

3 Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, (Poligono La Coma s/n), Paterna, Valencia, (46071), Spain

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BMC Genomics 2010, 11:181  doi:10.1186/1471-2164-11-181

Published: 17 March 2010

Additional files

Additional file 1:

Presence/absence of islands among the five considered genomes. The presence or absence of a given island (column headers) is reported for every genome (line). Orange island is common to all strain, blue islands are strain-specific islands, red islands are common to Lpa and Lpc genomes, the green island is present in Lpp, Lpg and Lpl but not in Lpa or Lpc genomes. For the other is not possible to make a clear hypothesis about their origin.

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Additional file 2:

CRISPR associated gene trees. Rooted trees obtained by neighbor joining method applying Kimura distance. In bold the Legionella pneumophila str. Alcoy sequence. Relative sequences represent best hits from GenBank protein refseq database.

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Additional file 3:

CRISPR repeats structure in Alcoy genome. Rooted trees obtained by neighbor joining method applying Kimura distance. In bold the Legionella pneumophila str. Alcoy sequence. Relative sequences represent best hits from GenBank protein Refseq database.

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Additional file 4:

Mvin gene trees. Rooted trees obtained by neighbor joining method applying Kimura distance. In bold the Legionella pneumophila str. Alcoy sequence. Relative sequences represent best hits from GenBank protein Refseq database.

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Additional file 5:

Bacilysin containing island from Alcoy genome. Bacilysin cluster begins with an ORF homolog of a phospho-2-dehydro-3-deoxyheptonate aldolase, which is an intermediate of the synthesis of chorismate (lpa03410); the next four ORFs are homologs of bacilysin biosynthesis BacA (lpa03409), BacB (lpa03408), BacC (lpa03407) and BacC (lpa03406); lpa03405 is a transporter of the multidrug/metabolite exporter family; lpa0304 is a purine metabolism-related protein. lpa03404 and lpa3403 are related to chorismate mutase and the subsequent amino-transferase could be related to the final steps in bacilysin biosynthesis [61]. Located further along the island, lpa03412 is a homolog of an S24-like peptidase, followed by two hypothetical proteins and a bacteriocin adenylyltransferase (lpa03416). The PR5 island ends with an IS10-related transposase, lpa03419, two hypothetical proteins and a phage related integrase (lpa03425). This island demonstrates evidence of cluster acting in bacilysin-like bacteriocin production that is specific to the Alcoy genome.

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Additional file 6:

Genomes used for rarefaction analysis. For each organisms strain names and GenBank accession numbers are reported.

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