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Open Access Highly Accessed Research article

Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae

Haruo Suzuki1, Tristan Lefébure12, Paulina Pavinski Bitar1 and Michael J Stanhope1*

Author Affiliations

1 Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA

2 Université de Lyon; UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France

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BMC Genomics 2012, 13:38  doi:10.1186/1471-2164-13-38

Published: 24 January 2012

Additional files

Additional file 1:

Supplementary Table S1. Genomic information of the 28 Staphylococcus strains and Macrococcus caseolyticus JCSCS5402. Supplementary Table S2. Gene content table for the 28 Staphylococcus strains and Macrococcus caseolyticus JCSCS5402. The first 13 columns contain the protein family identification number, partial sequence (0, no; 1, one side; 2, both sides), amino acid length (Laa), locus_tag or protein_id (tag), functional annotations from different databases: COG, GenBank, JCVI, KEGG, VFDB, MvirDB, Pfam, and GO. The remaining columns show binary data (1 or 0) for presence or absence of each protein family for each of the 29 strains. Supplementary Table S3. Protein families present in Staphylococcus aureus and absent in other Staphylococcus species, and vice versa. The first 13 columns are explained in Supplementary Table S2. Supplementary Table S4. Protein families present in Staphylococcus simiae and absent in other Staphylococcus species, and vice versa. The first 13 columns are explained in Supplementary Table S2. Supplementary Table S5. Database categories that are over- or underrepresented in Staphylococcus aureus relative to Staphylococcus simiae. a = the number of the S. aureus strains' protein families in this category, b = the number of the S. aureus strains' protein families not in this category, c = the number of the S. simiae strain's protein families in this category, d = the number of the S. simiae strain's protein families not in this category, odds ratio = ad/bc, p-value obtained by Fisher's exact test, and q-value (false discovery rate adjusted p-value).

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Additional file 2:

Supplementary Figure S1. A majority rule consensus of the maximum likelihood trees obtained from nucleotide sequences of the orthologous core genes for the 28 Staphylococcus strains and Macrococcus caseolyticus JCSCS5402 (outgroup). The percentages of genes that support the branches of the tree are indicated.

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Additional file 3:

Supplementary Figure S2. A heatmap showing % identity values of TBLASTN (E-value cutoff of 1e-5) best hits in the 28 Staphylococcus strains and Macrococcus caseolyticus JCSCS5402, against Staphylococcus virulence genes deposited in Virulence Factors Database (VFDB).

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