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Figure 1 | BMC Genetics

Figure 1

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

Figure 1

Genomic organization of VCBP1, 2, 4, 5 and VCBP3. A. Overlapping scaffolds_295 and 82 represent VCBP haplotypes B and A, respectively; assemblies are based on Brafl1, which was corrected from sequencing of BAC clones 62d19, 63n5-43b24 and 100J9. Information also derives from sequencing of additional BACs and PACs. VCBP1/4 is represented by a pair of artifactual gene duplicates on scaffold_295. BAC 100j9 possesses the second set of VCBP1/4 gene pairs (see Additional files 5 and 6) incorrectly assembled onto scaffold_295; correct assignment is scaffold_869 (haplotype A) (dotted arrow; authors note: assembly correction). The first set of VCBP1/4 genes on scaffold_295 is supported by direct PCR and limited DNA sequencing from BAC 5h9 (data not shown). The contiguous genetic region defined by haplotypes A (scaffold_82) and B (scaffold_295) spans ~1.5 Mb. PAC 37d15 (independent animal) represents haplotype C and possesses a VCBP2 CNV (VCBP 2a*); PAC 34i17, not shown, represents a unique VCBP1/4 haplotype. Shaded box (labeled YR) represents a Ngaro-like tyrosine recombinase retroposon gene (see text). Pseudogenes (Y) are indicated while intergeneic distances are in kb (1,000 base pairs) but not to scale. Transcriptional orientation is indicated by directionality of gene boxes; a and b designations reflect paralogous relationships. B. VCBP3 is located on scaffold_1; an independent PAC allele (see Additional files 7 and 10) exhibits allelic variation. Screening of the BAC library revealed two VCBP3 alleles localized to BACs 90f15 and 54h3 (see Additional file 8). CHEF analyses (not shown) and extensive BAC library screening are inconsistent with linkage between the VCBP1/4 and 2/5 clusters and the VCBP3 gene.

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