Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses

Additional file 1:

Genomic G+C content of different groups of LDVs.

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Additional file 2:

Genomic G+C content of the 67 LDVs.

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Additional file 3:

Comparison of the cA gene proportions with the total number of genes encoded in each LDV genomes.

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Additional file 4:

Comparison of the cA gene proportions with genomic G+C content.

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Additional file 5:

Comparison of the nucleotide composition between cA genes and host genes. We used genes from 61 LDV genomes with sufficient amount of host CDS data. For every viral gene, genomic signature distances (i.e. Euclidian distances based on di-nucleotide frequencies) from viral genome (horizontal axis) and from host genome (vertical axis) were computed. (A): non-cA genes. (B) and (C): cA genes. In (C), the vertical axis corresponds to the distance between the cA genes and a randomly chosen host genome.

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Additional file 6:

Sub-strand classification, according to their nucleotide-skew, for 15 LDV genomes.

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Additional file 7:

cA gene clusters of significant size in 11 LDV genomes.

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Additional file 8:

List of the cA genes in the 67 LDV genomes.

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Additional file 9:

Summary of viral genes involved in the control of host defense system.

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Additional file 10:

Phylogenetic trees supporting the HGT events for the cA genes detected by a composition-based approach. (A) Glutathione peroxidase, (B) Interleukin 10, (C) R1R hypothetical protein, (D) G protein-coupled receptor, (E) Photosystem II D2 protein, (F) Site-specific DNA methylase, (G) Thymidylate synthase and (H) Cytosine methyltransferase. Each node is labeled with SWISS-PROT/TrEMBL entry, the taxonomic group (A for Archaea, B for Bacteria, E for Eukaryota and V for Virus) and the specie name. The viral genes detected as cA genes by the method of the Nakamura et al. are highlighted in red. "I" corresponds to a clade branching with the viral cA genes; "O1" corresponds to the outgroup of I, and "O2" corresponds to the outgroup of I and O1. Paralogs, orthologs and homologs indicate the relationships between the outgroups (O1 or O2) and the internal groups (I or (I, O1)). (A-E) satisfy the criterion 1, and (F-H) satisfy the criterion 2 (see Methods). Tree reconstruction was carried out by the maximum likelihood method. Bootstrap values are indicated as the branch levels.

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Additional file 11:

Nucleotide sequence data for the hosts (or its close relatives) of the 67 LDVs.

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