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Table 1 Haplotypic organization of VCBP genes and alleles based on BAC and PAC assisted reassembly efforts.

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

Haplotype genes

Genomic scaffold BAC/PAC support

Alleles

Haplotype A

Scaffold_82; _869

 

   VCBP 5a

BAC 63n5-43b24 contig

VCBP5S2*01

   VCBP 2b

BAC 63n5-43b24 contig

VCBP2S1*02

   VCBP 5b

BAC 63n5-43b24 contig

VCBP5S1*02

   VCBP 4a

BAC 100j9

VCBP4S1*02

   VCPB 1a

BAC 100j9

VCBP1S1*02

   VCBP 1b

Note1

VCBP1S3*01

   VCBP 1c

 

VCBP1S2*01

Haplotype B

Scaffold_295

 

   VCBP 5a

BAC 62d19

VCBP5S2*02

   VCBP 2b

BAC 62d19

VCBP2S1*03

   VCBP 5b

BAC 62d19

VCBP5S1*03

   VCBP 4a

BAC 5h9

VCBP4S1*04

   VCBP 1a

BAC 5h9

VCBP1S1*03

   VCBP 1d

Note2

VCBP1S4*01

Haplotype C

Independent animal

 

   VCBP 5a

PAC 37d15

VCBP5S2*03

   VCBP 2b

PAC 37d15

VCBP2S1*04

   VCBP 5b

PAC 37d15

VCBP5S1*04

   VCBP 2a

PAC 37d15

VCBP2S2*01

Haplotype A/B: VCBP3

Scaffold_1

 

   VCBP3

BAC 90F15

VCBP3S1*02

   VCBP3

BAC 54h3

VCBP3S1*03

Haplotype X

Independent animal

 

   VCBP3

PAC 30b18

VCBP3S1*04

  1. Haplotypes and gene naming are consistent with Figure 1, where a, b, c, etc. are paralogous VCBP genes. In the absence of known genetic linkage, haplotypic assignment of VCBP3 alleles is not clear, relative to the other VCBPs, see Figure 1. Haplotype X is an independent animal from the same multi-animal library from which haplotype C was acquired, yet no relationship between the haplotypes is discernable. Accession numbers and downloadable sequences are available in Additional file 1. Note1 BAC support was not pursued for VCBP1b and VCBP1c. Note2 VCBP1d is a five exon pseudogene. BAC support was not pursued; a VCBP5-like pseudogene consisting of only the CBD exon is also present on haplotype A and B but not listed here, see Additional file 1.