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Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

Cecilia Alsmark12, Peter G Foster3, Thomas Sicheritz-Ponten4, Sirintra Nakjang1, T Martin Embley1* and Robert P Hirt1*

Author Affiliations

1 Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK

2 Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, S-751 23 Uppsala, Sweden

3 Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK

4 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby and Novo Nordisk Foundation Center for Biosustainability, DK-2900 Hørsholm, Denmark

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Genome Biology 2013, 14:R19  doi:10.1186/gb-2013-14-2-r19

Published: 25 February 2013

Additional files

Additional file 1:

Flowchart of methodology. Figure depicting the flowchart of the methodology used to identify lateral gene transfers (LGTs) including the number of genes retained at each step of the analysis for the 13 analyzed genomes.

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Additional file 2:

Prokaryote-to-eukaryote lateral gene transfers (LGTs). Table with the accession numbers and annotations of proteins for prokaryote-to-eukaryote LGTs supported in the Bayesian consensus trees by at least one node. For legends to the table, see Additional file 17; for illustrations of the trees, see Additional file 5.

Format: XLSX Size: 89KB Download file

Open Data

Additional file 3:

Eukaryote-to-eukaryote lateral gene transfers (LGTs). Table with the accession numbers and annotations of proteins for eukaryote-to-eukaryote LGTs supported in the Bayesian consensus trees by at least one node. For legends to the table, see Additional file 17; for illustrations of the trees, see Additional file 6.

Format: XLSX Size: 24KB Download file

Open Data

Additional file 4:

Eukaryote-to-prokaryote lateral gene transfers (LGTs). Table with the accession numbers and annotations of proteins for eukaryote-to-prokaryote LGTs supported in the Bayesian consensus trees by at least one node. For legends to the table, see Additional file 17; for illustrations of the trees, see Additional file 7.

Format: XLSX Size: 13KB Download file

Open Data

Additional file 5:

Phylogenetic trees supporting prokaryote-to-eukaryote lateral gene transfers (LGTs). Figure illustrating the phylogenies for the candidate LGTs from prokaryotes to eukaryotes supported by at least one well-supported node in the phylogenetic tree.

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Additional file 6:

Phylogenetic trees supporting eukaryote-to-eukaryote lateral gene transfers (LGTs). Figure illustrating the phylogenetic trees for the candidate LGTs from eukaryotes to prokaryotes supported by at least one well-supported node in the phylogenetic tree.

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Open Data

Additional file 7:

Phylogenetic trees supporting eukaryote-to-prokaryote lateral gene transfers (LGTs). Figure illustrating the phylogenetic trees for the candidate LGTs from eukaryotes to prokaryotes supported by at least one well-supported node in the phylogenetic tree.

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Additional file 8:

Comparison of lateral gene transfers (LGTs) detected in this and previous studies for individual taxa. Number of LGTs from this study contrasted with previously published LGTs cases for the target taxa. For all legends to the table, see Additional file 17.

Format: XLSX Size: 11KB Download file

Open Data

Additional file 9:

Relative numbers of lateral gene transfers (LGTs) to proteome size. Figure and table of the relationship between the number of identified LGTs and the number of annotated genes in each respective genome.

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Additional file 10:

Paralog counts for lateral gene transfers (LGTs). Estimated number of paralogs for each LGT listed in Supplementary Tables 1 to 3. For all legends to the table, see Additional file 17.

Format: XLSX Size: 47KB Download file

Open Data

Additional file 11:

Taxonomy of donors of lateral gene transfers (LGTs). Table with the counts for specific comparisons between selected target taxa for the functional categories of LGTs or the taxonomy of LGT donor lineages supported by a least one node. For all legends to the table, see Additional file 17.

Format: XLSX Size: 10KB Download file

Open Data

Additional file 12:

Taxonomy of donor lineages for candidate lateral gene transfer (LGT) between specific subsets of protists, with extended versions and additional comparison. Diagrams presenting comparisons of donor lineages for candidate LGTs between different groups of protists.

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Additional file 13:

Taxonomic counts of donors of lateral gene transfer (LGTs). Table with the counts of the taxonomy of the potential prokaryotic donor lineages for LGTs supported by at least one node (defined as the adjacent lineage to a given target taxa in trees (for list, see Additional file 2; for illustrations, see Additional file 5). For all legends to the table, see Additional file 17.

Format: XLSX Size: 9KB Download file

Open Data

Additional file 14:

Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations. Table with the number of proteins annotated in KEGG for all the 13 target genomes analyzed in this study and the corresponding diversity of KEGG entries for annotated enzymes. For all legends to the table, see Additional file 17.

Format: XLSX Size: 10KB Download file

Open Data

Additional file 15:

Lateral gene transfer (LGTs) affecting KEGG secondary metabolites and regulatory pathways. Figure illustrating the LGTs mapped onto the KEGG secondary metabolite and regulatory pathways.

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Additional file 16:

Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the degradation of gangliosides. Figure illustrating a schematic overview of the KEGG pathway for the degradation of gangliosides.

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Additional file 17:

Table legends. Legends for tables in additional files 2, 3, 4, 8, 10, 11, 13, and 14.

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