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Open Access Research article

Classification and nomenclature of all human homeobox genes

Peter WH Holland1*, H Anne F Booth1 and Elspeth A Bruford2

Author Affiliations

1 Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK

2 HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK

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BMC Biology 2007, 5:47  doi:10.1186/1741-7007-5-47

Published: 26 October 2007

Additional files

Additional file 1:

Maximum likelihood phylogenetic tree of all human plus selected protostome and cnidarian homeodomains for identification of gene families. Arbitrarily rooted phylogenetic tree of all human plus selected protostome and cnidarian homeodomains constructed using the maximum likelihood (ML) method. Bootstrap values supporting gene family designations are shown. Homeodomain sequences derived from pseudogenes are excluded. This ML tree should be compared with the neighbor-joining (NJ) tree shown in Additional file 2.

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Additional file 2:

Neighbor-joining phylogenetic tree of all human plus selected protostome and cnidarian homeodomains for identification of gene families. Arbitrarily rooted phylogenetic tree of all human plus selected protostome and cnidarian homeodomains constructed using the neighbor-joining (NJ) method. Bootstrap values supporting gene family designations are shown. Homeodomain sequences derived from pseudogenes are excluded. Comparison of NJ and ML trees, and description of the dataset used, is given in the legend to Additional file 1. Several artefactual mixing of classes occurs in this NJ tree, notably splitting of the CUT class, mixing of the TALE and SINE classes and aberrant placement of HOPX.

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Additional file 3:

Neighbor-joining phylogenetic tree of human ANTP-class homeodomains, for comparison to maximum likelihood tree. Arbitrarily rooted phylogenetic tree of human ANTP-class homeodomains constructed using the neighbor-joining method. Bootstrap values supporting internal nodes with over 70% are shown. Homeodomain sequences derived from pseudogenes are excluded. The proposed division between the HOXL and NKL subclasses is indicated. The position of EN1 and EN2 is unstable; this tree places them close to the base of the HOXL/NKL divergence, whereas maximum likelihood analysis of the same dataset places them firmly in the NKL subclass (Figure 1). Interrelationships of genes in the Nk2.2 and Nk4 families are also unstable (in this tree and Figure 1 respectively); in these cases synteny within and between genomes clearly resolves gene families. Detailed relationships between different gene families should not be inferred from this tree.

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Additional file 4:

Neighbor-joining phylogenetic tree of human PRD-class homeodomains, for comparison to maximum likelihood tree. Arbitrarily rooted phylogenetic tree of human PRD-class homeodomains constructed using the neighbor-joining method. Bootstrap values supporting internal nodes with over 70% are shown. Homeodomain sequences derived from pseudogenes are excluded, as are the partial homeodomains of PAX2, PAX5 and PAX8, and the HOPX homeodomain because its extremely divergent sequence destabilizes the overall tree topology. Roman numeral suffixes are used to distinguish multiple homeodomains encoded by a single Dux-family gene. Detailed relationships between different gene families should not be inferred from this tree.

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Additional file 5:

Neighbor-joining phylogenetic tree of human homeodomains excluding ANTP and PRD classes, for comparison to maximum likelihood tree. Arbitrarily rooted phylogenetic tree of human homeodomains excluding the ANTP and PRD classes constructed using the neighbor-joining method. Bootstrap values supporting internal nodes with over 70% are shown. Homeodomain sequences derived from pseudogenes are excluded. Roman numeral suffixes are used to distinguish multiple homeodomains encoded by a single gene. Classes and/or families are color coded as shown in the key. The LIM and ZF classes are not recovered as two distinct monophyletic groups, a result also found by maximum likelihood analysis (Figure 3). The multiple homeodomains of Zfhx-family proteins and Zhx/Homez-family proteins are also dispersed in the tree, presumably artefactually. Monophyly of the CUT class is not recovered in this tree, but is by maximum likelihood analysis (Figure 3). Detailed relationships between different gene families should not be inferred from this tree.

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Additional file 6:

Multiple sequence alignment of all human plus selected protostome and cnidarian homeodomains. The consensus homeodomain sequence (shown several times for reference) was derived from a compilation of 247 human homeodomain sequences. The three horizontal lines indicate the positions of the three alpha-helices. The numbering scheme refers to amino acid position in the canonical 60-amino-acid homeodomain; insertions relative to this sequence are shown when present. Black shaded resides are invariant between all human homeodomains within each class (or family in the case of the ZF homeodomains). Sequence accession numbers are shown. For each gene family designation, maximum likelihood and neighbor-joining bootstrap support values are indicated (see Additional files 1 and 2). These values are not shown if the gene family does not form a monophyletic group in phylogenetic analyses (in which case n/a is written) or if an invertebrate homolog could not be found.

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Additional file 7:

Phylogenetic input file. All human and invertebrate homeodomains used in phylogenetic analyses are shown, after alignment and removal of insertions to give a uniform 60-amino-acid alignment.

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