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Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants

Xiaofan Zhou123, Zhenguo Lin128 and Hong Ma1234567*

Author Affiliations

1 Department of Biology, the Pennsylvania State University, University Park, Pennsylvania 16802, USA

2 Institute of Molecular Evolutionary Genetics, the Pennsylvania State University, University Park, Pennsylvania 16802, USA

3 Intercollege Graduate Program in Cell and Developmental Biology, Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennsylvania 16802, USA

4 State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Handan Road, Shanghai 200433, PR China

5 Institute of Plant Biology, Fudan University, Handan Road, Shanghai 200433, PR China

6 Center for Evolutionary Biology, School of Life Sciences, Fudan University, Handan Road, Shanghai 200433, PR China

7 Institutes of Biomedical Sciences, Fudan University, Yixueyuan Road, Shanghai 200032, PR China

8 Current address: Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, Illinois 60637, USA

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Genome Biology 2010, 11:R38  doi:10.1186/gb-2010-11-4-r38

Published: 6 April 2010

Additional files

Additional file 1:

Supplemental Tables S1 to S7. Table S1: a summary of representative species included in this study. Table S2: a summary of MCL gene clustering results. Table S3: a summary of gene families known to have experienced early eukaryotic gene duplication. Table S4: test of the impact of long-branch attraction on orthogroups with vulnerable topologies. Table S5: distribution of orthogroups with phyletic patterns supporting early eukaryotic duplication - analysis I. Table S6: distribution of orthogroups with phyletic patterns supporting early eukaryotic duplication - analysis III. Table S7: results of MCL clustering analyses with genes from additional animal species.

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Additional file 2:

Information about all the gene clusters analyzed in analyses I, II and III, including gene cluster ID, accession number for each cluster member and information about whether the cluster exhibit early eukaryotic duplication with different phylogenetic methods and bootstrap support levels. In addition, for gene clusters analyzed with additional sequences from divergent protists, information about the protist species included in each cluster and the phyletic pattern is provided.

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Additional file 3:

Information about MCL clustering analyses with genes from additional animal species, including gene cluster ID and accession number of each cluster member. The gene clusters are also cross-referred to the clusters analyzed in analysis I/II and labeled with one of the following terms; 'same' - the new cluster contains the same members as the cluster analyzed in snalysis I/II, except for the genes from additional species; 'parent_set' - the new cluster contains all the genes in the cluster analyzed in analysis I/II, but not 'same'; 'subset' - all genes in the new cluster (except for genes from additional species) are included in the cluster analyzed in analysis I/II, but not 'same'; 'overlapping' - more than 50% genes in the new cluster (except for genes from additional species) are included in the cluster analyzed in analysis I/II, but not among the previous three types.

Format: XLS Size: 7.3MB Download file

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