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Gene duplication and fragmentation in the zebra finch major histocompatibility complex

Christopher N Balakrishnan18*, Robert Ekblom23, Martin Völker4, Helena Westerdahl5, Ricardo Godinez1, Holly Kotkiewicz6, David W Burt7, Tina Graves6, Darren K Griffin4, Wesley C Warren6 and Scott V Edwards1

Author Affiliations

1 Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA

2 Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK

3 Department of Population Biology and Conservation Biology, Uppsala University, Uppsala, Sweden

4 Department of Biosciences, University of Kent, Kent, UK

5 Department of Animal Ecology, Lund University, Lund, Sweden

6 School of Medicine, Genome Sequencing Center, Washington University, St Louis, MO, USA

7 Roslin Institute, Division of Genetics & Genomics, University of Edinburgh, Edinburgh, UK

8 Current address: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, USA

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BMC Biology 2010, 8:29  doi:10.1186/1741-7007-8-29

Published: 1 April 2010

Additional files

Additional file 1:

Overgo probes used for BAC library screening. Overgo probes targeting five genes of the MHC. Two pairs of probes were designed for each gene using sequences from the zebra genome trace archive.

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Additional file 2:

Self-self BLAST analysis of six BAC assemblies (Class II: A to D, Class I: E to F). Theses results highlight the repetitive nature of these genomic regions, and the challenges faced in assembly.

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Additional file 3:

Genes found by BAC sequencing. Genes found by BAC sequencing and manual and automated gene prediction.

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Additional file 4:

Two-color FISH mapping of TAP2 and MHC Class I BACs. Depicted is the only case in which BACs putatively containing TAP2 and Class I colocalised. Colocalisation was on the W chromosome.

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Additional file 5:

BACs used in two color FISH mapping. BACs used in dual-color FISH experiments with zebra finch MHC. These BACs are specific for zebra finch microchromosomes 9-15 and 17-28. None of these BACs cohybridized with MHC BACs. Because the whole genome assembly places some MHC genes on chromosome 22, we tested two chromosome 22 BACs. Both of these cohybridize with each other, and neither cohybridized with MHC BACs.

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Additional file 6:

Phylogenetic analysis and selection on MHC Class I sequences. A) Phylogenetic relationships among passerine MHC Class I, exon 3 sequences. Only one sequence with open reading frames were found in the zebra finch genome. The remaining sequences are from GenBank. B) Predicted amino acid sequences of the genomic sequence and one EST for MHC Class I. Stars represent sites showing evidence of selection in passerine birds. Note the similarity in the selected sites between raptors and passerines, both of which correspond well with the human PBR.

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Additional file 7:

Preparation of chicken chromosomes. The method for the preparation of chicken chromosome spreads is described.

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