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Open Access Research article

Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus

Larry J Dishaw12, M Gail Mueller1, Natasha Gwatney3, John P Cannon23, Robert N Haire3, Ronda T Litman3, Chris T Amemiya4, Tatsuya Ota5, Lee Rowen6, Gustavo Glusman6 and Gary W Litman123*

Author Affiliations

1 All Children's Hospital, Department of Molecular Genetics, 801 Sixth Street South, St. Petersburg, FL 33701, USA

2 H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA

3 Department of Pediatrics, University of South Florida College of Medicine, USF/ACH Children's Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA

4 Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA 98101, USA

5 Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Kamiyamaguchi 1560-35, Hayama 240-0193 Japan

6 Institute for Systems Biology, 1441 N. 34th St, Seattle, WA, 98103, USA

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BMC Genetics 2008, 9:78  doi:10.1186/1471-2156-9-78

Published: 1 December 2008

Abstract

Background

The variable region-containing chitin-binding proteins (VCBPs) are found in protochordates and consist of two tandem immunoglobulin variable (V)-type domains and a chitin-binding domain. We previously have shown that these polymorphic genes, which primarily are expressed in the gut, exhibit characteristics of immune genes. In this report, we describe VCBP genomic organization and characterize adjacent and intervening genetic features which may influence both their polymorphism and complex transcriptional repertoire.

Results

VCBP genes 1, 2, 4, and 5 are encoded in a single contiguous gene-rich chromosomal region and VCBP3 is encoded in a separate locus. The VCBPs exhibit extensive haplotype variation, including copy number variation (CNV), indel polymorphism and a markedly elevated variation in repeat type and density. In at least one haplotype, inverted repeats occur more frequently than elsewhere in the genome. Multi-animal cDNA screening, as well as transcriptional profilingusing a novel transfection system, suggests that haplotype-specific transcriptional variants may contribute to VCBP genetic diversity.

Conclusion

The availability of the Branchiostoma floridae genome (Joint Genome Institute, Brafl1), along with BAC and PAC screening and sequencing described here, reveal that the relatively limited number of VCBP genes present in the amphioxus genome exhibit exceptionally high haplotype variation. These VCBP haplotypes contribute a diverse pool of allelic variants, which includes gene copy number variation, pseudogenes, and other polymorphisms, while contributing secondary effects on gene transcription as well.