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

doi:10.1186/1471-2156-9-78

BMC Genetics

Volume 9

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Dishaw LJ
Mueller MG
Gwatney N
Cannon JP
Haire RN
Litman RT
Amemiya CT
Ota T
Rowen L
Glusman G
Litman GW

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Dishaw LJ
Mueller MG
Gwatney N
Cannon JP
Haire RN
Litman RT
Amemiya CT
Ota T
Rowen L
Glusman G
Litman GW
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Research article

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

Larry J Dishaw¹^,2 , M Gail Mueller¹ , Natasha Gwatney³ , John P Cannon²^,3 , Robert N Haire³ , Ronda T Litman³ , Chris T Amemiya⁴ , Tatsuya Ota⁵ , Lee Rowen⁶ , Gustavo Glusman⁶ and Gary W Litman¹^,2^,3

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

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

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

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

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

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

author email corresponding author email

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


Published:	1 December 2008

Additional files

Additional file 1:

Tabular description of BAC and PAC sequences, VCBP pairwise comparisons, and annotation. Table S1. Characterization of new VCBP alleles from genomic resource animal and additional animal PAC library-derived clones. Table S2. BAC and PAC clones used to aid in the genomic description, annotation, and validation of the VCBP genomic region of Brafl1. Table S3. Pairwise comparison (identity | similarity percentages) of deduced amino acid sequences for the VCBPs that are supported by BAC and PAC evidence. Table S4. Pairwise nucleotide identity among all alleles described in Figure 1. Table S5. Annotation of coding regions and predicted genes from the VCBP-containing BAC and PAC clones described. Complete list of transcripts is included.

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Additional file 2:

Dot plot pairwise comparison of the VCBP2/5 cluster containing BAC clones, 62d19 and 63n5-43b24 contig (haplotype B and A, respectively), reveals extensive polymorphism.

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Additional file 3:

Dot plot pairwise comparison of BAC 62d19 and BAC contig 63n5-43b24 exhibits discontinuities associated with allelic polymorphism, notably across the region encoding the VCBP2/5 cluster.

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Additional file 4:

Dot plot pairwise comparison of the reverse complement of BAC 62d19 and BAC contig 63n5-43b24, and the corresponding region of the amphioxus genome.

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Additional file 5:

Dot plot pairwise comparison of the reverse complement of the VCBP1/4-containing BAC 100j9 with the corresponding region of scaffold_295.

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Additional file 6:

Dot plot pairwise comparisons of scaffold_295 and scaffold_869 with the reverse complement of BAC 100j9 and PAC 34i7 (independent animal haplotype).

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Additional file 7:

Dot plot pairwise comparisons of the reverse complement of a ~100 kb region of scaffold_1 encoding VCBP3 with the corresponding region from BAC 90f15 and BAC 54h3, as well as PAC 30b18 (independent animal haplotype) encoding VCBP3.

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Additional file 8:

Dot plot comparisons of the VCBP3 gene region reveals that BAC 90f15 corresponds to genomic scaffold_1 (A) and that the other allele is highly polymorphic (B).

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Additional file 9:

Genomic organization of the tyrosine recombinase domain-encoding retroelement found adjacent to the VCBP2/5 cluster.

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Additional file 10:

Genomic representation (using the Gestalt viewer) across the BAC and PAC alleles described in this study.

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