Open Access Highly Accessed Research article

Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

Torsten Hain1, Rohit Ghai1, André Billion1, Carsten Tobias Kuenne1, Christiane Steinweg1, Benjamin Izar1, Walid Mohamed1, Mobarak Abu Mraheil1, Eugen Domann1, Silke Schaffrath1, Uwe Kärst2, Alexander Goesmann3, Sebastian Oehm3, Alfred Pühler3, Rainer Merkl4, Sonja Vorwerk5, Philippe Glaser6, Patricia Garrido7, Christophe Rusniok7, Carmen Buchrieser7, Werner Goebel8 and Trinad Chakraborty1*

Author Affiliations

1 Institute of Medical Microbiology, Justus-Liebig-University, Schubertstrasse 81, Giessen, D-35392, Germany

2 Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, Braunschweig, 38124, Germany

3 Center for Biotechnology, University of Bielefeld, Bielefeld, D-33594, Germany

4 Institut für Biophysik und physikalische Biochemie, Universität Regensburg, Universitätstrasse 31, Regensburg, D-93053, Germany

5 Febit Biomed GmbH, Im Neuenheimer Feld 519, Heidelberg, D-69120, Germany

6 Institut Pasteur, Laboratoire Evolution et Génomique Bactériennes and CNRS URA 2171, Paris, 75724, France

7 Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS URA 2171, Paris, 75724, France

8 Max von Pettenkofer-Institut for Hygiene and Medical Microbiology, Ludwig Maximilians-University München, Pettenkoferstrasse 9a, Munich, D-80336, Germany

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BMC Genomics 2012, 13:144  doi:10.1186/1471-2164-13-144

Published: 24 April 2012

Additional files

Additional file 1 :

Table S1. Nucleotide analysis of actA repeats of Listeria.

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Additionaf file 2 :

Table S2. Prediction of LRR region containing proteins by Augur [90].

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Additional file 3 :

Table S2. Prediction of proteins containing GW modules by Augur [90].

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Additional file 4 :

Table S4. Prediction of LPXTG motif harbouring proteins by Augur [90].

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Additional file 5 :

Table S5. Prediction of lipoproteins by Augur [90].

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Additional file 6 :

Table S6. Prediction of LysM domain containing proteins by Augur [90].

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Additional file 7 :

Table S7. Prediction of NLPC/P60 domain containing proteins by Augur [90].

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Additional file 8:

Table S8. Comparative CRISPR analysis table.

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Additional file 9:

Table S9. Metabolosome of L. monocytogenes 1/2a EGD-e.

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Additional file 10:

Table S10. Primers used in this study.

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Additional file 11:

Figure S1. Comparative analysis of L. monocytogenes ActA protein sequences.

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Additional file 12:

Figure S2. Comparison of the inlGHE locus in the three listerial lineages. All three genes in this cluster have been absent in the L. monocytogenes 4a L99 genome.

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Additional file 13:

Figure S3. Genome analysis of lmaDCBA region of six listeriae. Comparative analysis was performed using GECO [82] applying bidirectional pairs.

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Additional file 14:

Figure S4. Frequency of distributions of the percentage identity between all duplicated gene pairs in the Listeria genomes.

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Additional file 15:

Figure S5. Gene duplication and horizontal gene transfer in Listeria genomes.

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Additional file 16:

Figure S6. Duplication vs. HGT classifiable genes in listeriae.

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Additional file 17 :

Figure S7. Complete PTS Systems in L. monocytogenes strains.

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Additional file 18:

Figure S8. Partial PTS Systems in L. monocytogenes strains.

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Additional file 19:

Text S1. SNP analysis of three listerial lineages.

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Additional file 20:

Text S2. Differential regulation of glycolysis in L. monocytogenes 4b F2365.

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Additional file 21:

Text S3. Comparison of two L. monocytogenes 4b strains CLIP80459 and F2365.

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Additional file 22:

Figure S9. Confirmation of lacking genes encoding surface proteins in four L. monocytogenes 4a strains and three L. monocytogenes 4c strain generated by PCR analysis.

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Additional file 23:

Figure S10. Intracellular flagellin expression data of L. monocytogenes 1/2a EGD-e, L. monocytogenes 4a L99, L. monocytogenes 4b CLIP80459 and L. monocytogenes 4b F2365 generated by qRT-PCR analysis.

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Additional file 24:

Figure S11. List of gene duplication in Listeria genomes.

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