Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach

doi:10.1186/1471-2148-8-67

BMC Evolutionary Biology

Volume 8

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Research article

Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach

Kirsten A Bratke and Aoife McLysaght

Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland

author email corresponding author email

BMC Evolutionary Biology 2008, 8:67doi:10.1186/1471-2148-8-67


Published:	27 February 2008

Additional files

Additional file 1:

Conserved Poxvirus Synteny. Horizontal lines represent completely sequenced genomes with genes on the 5'-3' strand and 3'-5' strand represented as blocks above and below the line, respectively. Vertical lines connect genes in different poxviruses that belong to single-copy families conserved in all poxviruses (red lines), all chordopoxviruses (blue lines) and the genus in question (yellow lines). One major inversion between avipox and other chordopox is noticeable, as well as excessive rearrangements in the entomopox lineage, where synteny breaks down. In all other places, synteny is extremely well conserved between genomes.

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Additional file 2:

Interleukin-10 Phylogeny. Phylogenetic trees for poxvirus Interleukin-10 and representative non-pox homologs. (A) NJ tree based on amino acid alignment (B) ML tree based on amino acid alignment. Branch lengths are not to scale. (C) ML tree based on nucleotide alignment (gaps copied from amino acid alignment). Branch lengths are not to scale. Tip labels indicate GenBank GI and the common species name for each sequence. Numbers on branches are bootstrap values out of 1000 for NJ tree (A) and out of 100 for ML trees (B and C).

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Additional file 3:

IL10 multiple sequence alignment. Each sequence is labelled with its NCBI GI. This image was created using JalView: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview Java Alignment Editor," Bioinformatics, 20, 426-7

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Additional file 4:

Synteny conservation around TK in poxvirus genomes. As for Fig. 2. The gene of interest, TK, is colored red with a bold outline. (A) Neighborhood with respect to "core families"; (B) Neighborhood with respect to "ortholog families"; (C) Neighborhood with respect to "ortho-para families".

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Additional file 5:

Synteny conservation around RRS in poxvirus genomes. As for Fig. 2. The gene of interest, RRS, is colored red with a bold outline. Neighborhood with respect to core families.

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Additional file 6:

Synteny conservation around GP in poxvirus genomes. As for Fig. 2. The gene of interest, GP, is colored red with a bold outline. Neighborhood with respect to ortholog families.

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Additional file 7:

Synteny conservation around DP in poxvirus genomes. As for Fig. 2. The gene of interest, DP, is colored red with a bold outline. Neighborhood with respect to core families.