Open Access Highly Accessed Research article

Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution

Claus Kemkemer14, Matthias Kohn1, David N Cooper2, Lutz Froenicke3, Josef Högel1, Horst Hameister1 and Hildegard Kehrer-Sawatzki1*

Author Affiliations

1 Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany

2 Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK

3 Dept. of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA

4 LMU München, Biozentrum Martinsried, München, Germany

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BMC Evolutionary Biology 2009, 9:84  doi:10.1186/1471-2148-9-84

Published: 24 April 2009

Additional files

Additional file 1:

Summary of E-painting results for human chromosomes 1–22. The conversion of the syntenic segment associations into colour-coded ideograms rendered the conserved syntenic segments (and at the same time, the breakpoint intervals) readily identifiable The human chromosome coordinates of the breakpoint intervals are given to the right of the human ideogram in Mb. The chromosome numbers of the orthologous segments in the analyzed species are indicated to the right of the conserved segments. Chromosomal breakpoints have been evenly spaced in order to facilitate visualization of the conserved syntenic segments. The resulting ideograms of the chromosomes and conserved segments are therefore not drawn to scale. The centromeric region is indicated by a black horizontal bar. The stippled red lines indicate breaks present in all analyzed vertebrate genomes which may therefore be attributed to rearrangements in the primate lineage.

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Additional file 2:

Summary of the evolutionary breaks for all human autosomal chromosomes. The breakpoint intervals are demarcated by the last gene from the proximal segment of conserved synteny and the first gene of the distal segment of conserved synteny. For some breaks, a duplication of the gene at the breakpoint was noted (duplicated genes). The breaks specific to the primate lineage are marked in yellow. For these primate-specific breaks, the links to copy number variants (CNV) and segmental duplications (SD) contained within the break intervals have been added. In the last column, the cancer-associated genes which flank evolutionary breaks (these genes are included within the respective segments of common synteny) and the known cancer-associated genes localized within the break intervals (see Table 5) are given.

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Additional file 3:

Phylogenetic relationships among the species investigated in this study and the armadillo and the elephant not analysed here (marked with an asterisk) according to Wildman et al. [65]. Scheme to indicate phylogenetic relationships between clades.

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Additional file 4:

Average transcript density of all evolutionary breakpoint intervals on human chromosomes. Table indicating the average transcript density of all evolutionary breakpoint intervals.

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Additional file 5:

Average transcript density of evolutionary breakpoint intervals mapped to regions under 40 kb (n = 144). Table indicating the average transcript density of evolutionary breakpoints.

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Additional file 6:

Results of 100,000 simulation experiments designed to investigate the question of random or non-random breakage during mammalian karyotype evolution. Table indicating the results of 100,000 simulation experiments designed to investigate the question of random or non-random breakage during mammalian karyotype evolution.

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