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Open Access Research article

High divergence in primate-specific duplicated regions: Human and chimpanzee Chorionic Gonadotropin Beta genes

Pille Hallast1, Janna Saarela2, Aarno Palotie345 and Maris Laan1*

Author Affiliations

1 Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia

2 Department of Molecular Medicine, National Public Health Institute, Haartmaninkatu 8, 00290 Helsinki, Finland

3 Finnish Genome Center, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland

4 The Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, MA 02142, USA

5 Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

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BMC Evolutionary Biology 2008, 8:195  doi:10.1186/1471-2148-8-195

Published: 7 July 2008

Additional files

Additional file 1:

Table for sequence parameters. Sequence parameters for the intergenic regions and for the whole LHB/CGB cluster in human and chimpanzee.

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Additional file 2:

Distribution of species-specific indels. For simplification we defined all identified gaps in sequence alignments of human and chimpanzee LHB/CGB region orthologous segments (Figure 1B) as deletions in one of the species. The figure shows the number of species-specific gaps (Y-axes) relative to their length in base pairs (X-axis) and the contribution of each deletion class (1–5; 6–10; 11–15; 16–20; 20–25; >100 bp) to the total length of species-specific gapped sequence.

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Additional file 3:

Table for nucleotide sequence divergence. Nucleotide sequence divergence in orthologous human and chimpanzee LHB/CGB genes. Divergence was estimated by using the human (GenBank: NG_000019) and chimpanzee (this study, Genbank: EU000308) reference sequences alone or by incorporating the re-sequencing data for one or both species (for human n = 95 [29]; for chimpanzee, n = 11, unpublished data of the authors) into the calculations.

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Additional file 4:

Table of estimated dn and ds values by Li93 method. Application of Li93 method [40,41] for estimating non-synonymous (dn) and synonymous (ds) substitutions, and amino acid divergence in human and chimpanzee orthologous genes and for testing significance in the deviation of dn/ds ratio from expectation under neutrality.

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Additional file 5:

Results of the CRANN analyses of human and chimpanzee orthologous genes (A) LHB, (B) CGB5, (C) CGB8, (D) CGB7, (E) CGB1. Results of moving window analysis carried out with CRANN [47,48]. X-axis shows the successive windows of 20 codon sites (window size: 20 codons, shift size: 10 codons). As the number of substitutions calculated in each moving window for human and chimpanzee orthologous genes was low, the dn and ds values were mostly zero and thus the dn/ds ratio was not shown.

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Additional file 6:

Primer sequences. Primers for sequencing of subcloned BACs 68P2 and 109B10 originating from common chimpanzee (Pan troglodytes) BAC library RPCI-43 (BACPAC Resource Center at the Children's Hospital Oakland Research Institute; Oakland, CA).

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Additional file 7:

Alignments of the chimp and human LHB/CGB transcripts. The aligned sequences of the major transcripts of the chimp and human LHB/CGB genes. The ATG of each gene has been indicated in red and underlined font. Translation STOP codons have been boxed.

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