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Open Access Highly Accessed Research article

Origin, evolution and classification of type-3 copper proteins: lineage-specific gene expansions and losses across the Metazoa

Felipe Aguilera, Carmel McDougall and Bernard M Degnan*

Author Affiliations

Centre for Marine Science, School of Biological Science, The University of Queensland, Brisbane, Queensland, 4072, Australia

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BMC Evolutionary Biology 2013, 13:96  doi:10.1186/1471-2148-13-96

Published: 1 May 2013

Additional files

Additional file 1:

Dataset: List of accession numbers, genome localisation and protein nomenclature used in this study. Accession numbers from Genbank and genomic localisations from Joint Genome Institute (JGI) and Bioinformatics Online Genome Annotation Services (BOGAS) for type-3 copper protein sequences.

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Open Data

Additional file 2:

Phylogenetic trees: Phylogenetic analyses of the α-subclass copper proteins. A. Neighbor-Joining (NJ) phylogenetic tree is shown. Statistical support for each node is indicated as percentage (1,000 bootstrap reanalyses). B. Maximum-Likelihood (ML) phylogenetic tree is shown. Statistical support for each node is indicated as percentage (1,000 bootstrap reanalyses). C. Bayesian Inference (BI) phylogenetic tree is shown. Statistical support for each node is indicated as posterior probabilities (2,500,000 generations). In all cases, trees were rooted by midpoint rooting and labelled as in Figure 2A.

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Additional file 3:

Phylogenetic trees: Phylogenetic analyses of the β-subclass copper proteins. A. Neighbor-Joining (NJ) phylogenetic tree is shown. Statistical support for each node is indicated as percentage (1,000 bootstrap reanalyses). B. Maximum-Likelihood (ML) phylogenetic tree is shown. Statistical support for each node is indicated as percentage (1,000 bootstrap reanalyses). C. Bayesian Inference (BI) phylogenetic tree is shown. Statistical support is indicated as posterior probabilities (2,500,000 generations). In all cases, trees were rooted by midpoint rooting and labelled as in Figure 2A.

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Additional file 4:

Phylogenetic trees: Phylogenetic analyses of the γ-subclass copper proteins. Neighbor-Joining (NJ) phylogenetic tree is shown. Statistical support for each node is indicated as percentage (1,000 bootstrap reanalyses). B. Maximum-Likelihood (ML) phylogenetic tree is shown. Statistical support for each node is indicated as percentage (1,000 bootstrap reanalyses). C. Bayesian Inference (BI) phylogenetic tree is shown. Statistical support is indicated as posterior probabilities (2,500,000 generations). In all cases, trees were rooted by midpoint rooting and labelled as in Figure 2A.

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Additional file 5:

Lineage-specific expansion of type-3 copper gene subclasses and their physical linkage: Putative physical linkages of some representatives from α-, β-, and γ-subclasses. Type-3 copper genes that are physically linked. Exons are indicated by boxes; while introns are indicated by lines adjoining these. Copper-binding sites A and B are indicated by black boxes Cu(A) at the left and Cu(B) at the right, respectively. Intergenic distances are indicated in kilobases. All gene structures are drawn to scale but these scales differ between phyla and subclasses. The arrow indicates the direction of transcription for each gene.

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