Open Access Research article

Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways

Anthony R Borneman*, Jane M McCarthy, Paul J Chambers and Eveline J Bartowsky

Author Affiliations

The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia 5064, Australia

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BMC Genomics 2012, 13:373  doi:10.1186/1471-2164-13-373

Published: 3 August 2012

Additional files

Additional file 1:

Super contig structure. Describes the position of each sequencing contig within the chromosomal super contigs in each strain.

Format: TXT Size: 46KB Download file

Open Data

Additional file 2:

Syntenic alignment and annotation of O. oeni open reading frames. Contains information regarding orthology relationships and gene function for open reading frames from each O. oeni strain for which sequencing data is available.

Format: XLS Size: 3.1MB Download file

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Open Data

Additional file 3:

Non-PSU-1 open reading frames. Contains full positional and orthology information for all of the open reading frames not found in the “reference” strain PSU-1.

Format: XLS Size: 554KB Download file

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Open Data

Additional file 4:

Genome-wide results of the “alien hunter” algorithm for each strain. Each individual plot has been spaced according to the whole-genome alignments to ensure that genomic regions are concordant across strains. The area of highest probability of HGT is indicated (black arrow).

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Open Data

Additional file 5:

Horizontal gene transfer events between O. oeni and Lactococcus spp. A representative protein (query_id) for each pan_genome locus was used in homology searches against the combined predicted protein sequences from each Lactococcus spp. genome (seq_id) available in Genbank. Average identity values were calculated using a 10 ORF sliding window (average(n = 10)). Regions in which >5 adjacent ORFs displayed >90% amino acid identity between an O. oeni protein and a protein from Lactococcus spp. are also indicated (window n = 5; identity > = 90).

Format: XLS Size: 973KB Download file

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Open Data

Additional file 6:

Exopolysaccharide gene clusters. Contains full positional and orthology information for all of the open reading frames predicted to encode members of the strain-dependent cell wall clusters.

Format: XLS Size: 53KB Download file

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Open Data

Additional file 7:

A novel glycosidase-PTS gene fusion. BLAST homology information for the glycosidase-PTS gene fusion predicted to be encoded by pan_genome ORF 2351. (PDF 44 kb)

Format: PDF Size: 45KB Download file

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Open Data