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


CONCLUSIONS
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.
Dishaw
Larry J
LJ
All Children's Hospital, Department of Molecular Genetics, 801 Sixth Street South, St, Petersburg, FL 33701, USA. ldishaw@health.usf.edu
Mueller
M Gail
MG
Gwatney
Natasha
N
Cannon
John P
JP
Haire
Robert N
RN
Litman
Ronda T
RT
Amemiya
Chris T
CT
Ota
Tatsuya
T
Rowen
Lee
L
Glusman
Gustavo
G
Litman
Gary W
GW
D000818:Animals; D002352:Carrier Proteins / Q000235:genetics*; D002686:Chitin / Q000378:metabolism*; D002816:Chordata, Nonvertebrate / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D018628:Gene Dosage; D014644:Genetic Variation; D016678:Genome; D006239:Haplotypes; D007135:Immunoglobulin Variable Region / Q000235:genetics*; D008957:Models, Genetic; D011110:Polymorphism, Genetic; D014158:Transcription, Genetic
D002352:Carrier Proteins; D007135:Immunoglobulin Variable Region; D002686:Chitin