Open Access Research article

Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome

Carsten Kuenne1, André Billion1, Mobarak Abu Mraheil1, Axel Strittmatter2, Rolf Daniel2, Alexander Goesmann3, Sukhadeo Barbuddhe4, Torsten Hain1* and Trinad Chakraborty1*

Author Affiliations

1 Institute of Medical Microbiology, German Centre for Infection Research, Justus-Liebig-University, D-35392, Giessen, Germany

2 Department of Genomic and Applied Microbiology and Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Goettingen, Grisebachstrasse 8, D-37077, Goettingen, Germany

3 Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, D-33549, Bielefeld, Germany

4 ICAR Research Complex for Goa, Ela, Old Goa, 403402, India

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BMC Genomics 2013, 14:47  doi:10.1186/1471-2164-14-47

Published: 22 January 2013

Additional files

Additional file 1:

Species homology matrices. General homology matrices showing the distribution of all coding sequences among 16 strains of species L. monocytogenes and 19 strains of genus Listeria at different cutoffs. This table is sorted for maximum conservation (core genes = top, specific genes = bottom).

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Additional file 2:

Insertional hotspot ranges. Hotspots showing at least three separate insertions denoted by locustag ranges.

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Additional file 3:

Comparative genomic GECO figures of hyper variable hotspots. Comparative GECO depictions of insertional hotspots highlighting extensive mosaicism.

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Additional file 4:

Mobile genetic elements. Distribution of mobile genetic elements ordered by relative position in the chromosome of L. monocytogenes 1/2a EGD-e.

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Additional file 5:

Comparative genomic GECO figures of transposons ICELm1 and TN554. Comparative GECO depiction using a homology measure of 60% amino acid identity and 80% coverage. Displays content and conservation of two transposons.

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Additional file 6:

Comparative genomic GECO figures of IS3 elements. Comparative GECO depiction using a homology measure of 60% amino acid identity and 80% coverage. Displays duplication of IS3-like transposon.

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Additional file 7:

Comparative genomic GECO figure of CRISPR/Cas loci. Comparative GECO depictions of three CRISPR/Cas loci using a minimum CDS homology measure of 60% amino acid identity and 80% coverage.Cas genes and spacer/repeat arrays are framed. Locus 1 displayed no associated Cas genes. Locus 3 includes a trans-acting sRNA called tracrRNA that was described to compensate for a missing endoribonuclease in conjunction with host factor RNase III.

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Additional file 8:

CRISPR/Cas loci. Homology matrices and positions of CRISPR/Cas genes and associated arrays of three loci. Spacers were additionally mapped versus the NCBI nt database to identify possible target sequences.

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Additional file 9:

Known virulence genes. Homology matrix of known virulence genes.

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Additional file 10:

Galleria standard deviations. Standard deviations calculated for independent experiments considering mortality rates of Galleria mellonella larvae over the course of seven days post infection.

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Additional file 11:

Growth curves BHI. Growth of L. monocytogenes in BHI medium at 37°C.

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Additional file 12:

Detailed analyses of reductive evolution of virulence-associated genes. In-depth information about previously described virulence and pathogenicity indicated genes that are absent or truncated in one of the compared strains.

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Additional file 13:

Plot of Surface-associated CDS. Bar plot depicting the distribution of all surface-associated protein coding genes among studied strains.

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Additional file 14:

Distribution of surface-associated genes displays conserved lineage-backbones with strain-specific adaptations. Detailed analysis of presence and absence of surface-associated genes.

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Additional file 15:

Surface-associated CDS. Homology matrices of genes containing a surface-associated domain (NLPC/p60, LysM, GW, LRR, LPxTG, Lipobox, signal peptide).

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Additional file 16:

Internalins. Homology matrix of genes containing a leucine rich repeat domain and an optional signal peptide.

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Additional file 17:

Putative transposition of lipoproteins lmo1264-5 in lineage III. Comparative GECO depiction using a homology measure of 80% amino acid identity and 90% coverage. Displays the putative transposition of lipoproteins lmo1264-5 in lineage III into the locus that putatively held inlC previously.

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Additional file 18:

Lineage-specific CDS. Homology matrix of coding genes specifically present in one lineage.

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Additional file 19:

Lineage I/II exclusive CDS. Homology matrix of genes conserved in 13/14 strains of lineages I and II, while being absent from both strains of lineage III.

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Additional file 20:

Serogroup and –type ancestral indels. Homology matrix of CDS found to be commonly present or absent (ancestral indel) for either one or multiple serogroups or -types.

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Additional file 21:

Strain-specific CDS. Homology matrix of coding genes specifically present in one strain.

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Additional file 22:

Small non-coding regulatory RNAs. Homology matrix of sRNA candidates.

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