Open Access Highly Accessed Research article

Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar

Motoshige Yasuike1, Johan de Boer1, Kristian R von Schalburg1, Glenn A Cooper1, Linda McKinnel1, Amber Messmer1, Stacy So1, William S Davidson2 and Ben F Koop1*

  • * Corresponding author: Ben F Koop bkoop@uvic.ca

  • † Equal contributors

Author Affiliations

1 Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, British Columbia, V8W 3N5, Canada

2 Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A1S6, Canada

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BMC Genomics 2010, 11:486  doi:10.1186/1471-2164-11-486

Published: 2 September 2010

Additional files

Additional file 1:

Features of the IGH-A. Table listing genes and pseudogenes identified in the IGH-A.

Format: XLS Size: 41KB Download file

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Additional file 2:

Features of the IGH-B. Table listing genes and pseudogenes identified in the IGH-B.

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Additional file 3:

The identified genes flanking the loci. Table listing genes flanking the loci identified with the Digit Web Server (http://synthetic-biology.jp/sw/pic/en/crib151s2rib151s72i/ webcite).

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Additional file 4:

Dotter plot of locus A (IGH-A) versus locus B (IGH-B). This file contains a dotter plot of IGH-A versus IGH-B.

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Additional file 5:

Alignment of amino acid sequences encoded by (A) Cτ, (B) C μ and (C) Cδ. This file contains multiple sequence alignments of amino acid sequences encoded by (A) Cτ, (B) C μ and (C) Cδ obtained from ClustalW. Identical residues are shown as dots (.) and gaps are shown as hyphens (-).

Format: PDF Size: 146KB Download file

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Additional file 6:

Phylogenic relationships for the CH genes in various species. Phylogenic tree showing the relationship of the CH genes amino acid sequences of CH2 and CH3 domains of α, human δ and γ; CH3 and CH4 of μ, ζ/τ, ε, and duck α; CH4 and CH5 of new antigen receptor (NAR); CH5 and CH6 of ω, NARC and teleost δ. The tree was constructed with the MEGA 4 package by neighbor-joining (NJ) method and bootstrap values for replicated 1,000 were represented by percentages on the edge of node. The bootstrap values greater than 50% are presented. The scale bar indicates the branch length. Genbank accession numbers are as follows: α: duck [GenBank:AAA68606], human [GenBank:AAC82528]. δ: Atlantic salmon δA and δB [GenBank:AF278717; AF141605], catfish [GenBank:T18537], fugu [GenBank:BAD34542], zebrafish [GenBank:CAI11477], Xenopus [GenBank:DQ350886], human [GenBank:AAA52771]. ε: human [GenBank:AAB59395], opossum (Monodelphis domestica) [GenBank:AAC79674]. γ1: human [GenBank:AAC82527]. γ3: mouse [GenBank:AAB59697]. μ: Atlantic salmon μA and μB, [GenBank:AAB24064; AAF69490], bowfin (Amia calva) [GenBank:ACU12456], carp [GenBank:AB004105], catfish [GenBank:M27230], gar (Lepisosteus osseus) [GenBank:U12455], ladyfish (Elops saurus) [GenBank:M26182] lungfish (Protopterus aethiopicus) [GenBank:AF437724] nurse shark (Ginglymostoma cirratum) [GenBank:M92851], rainbow trout [GenBank:X83372], skate (Leucoraja erinacea) [GenBank:M29679], sturgeon (Acipenser baeri) [GenBank:Y13253], zebrafish [GenBank:AY643753], Xenopus [GenBank:M20484], chicken [GenBank:X01613], mouse [GenBank:J00443], human [GenBank:X14940]. υ: Xenopus [GenBank:X15114]. ω: lungfish [GenBank:AF437727], sandbar shark (Carcharhinus plumbeus) [GenBank:CPU40560]. NAR: nurse shark [GenBank:GCU51450]. NARC: nurse shark [GenBank:GCU18701]. ζ/τ: grass carp (Ctenopharyngodon idella) [GenBank:DQ489733], rainbow trout τ1 and τ2 [GenBank:AAW66978] and [GenBank:AAW66981], perch (Siniperca chuatsi), [GenBank:DQ016660], zebrafish [GenBank:AY643752].

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Additional file 7:

Genbank accession numbers for deduced amino acid sequences of CH and VH domains. Table listing the accession numbers for deduced amino acid sequences of CH and VH domains.

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Additional file 8:

Alignment of D sequences. This file contains a multiple sequence alignment of D sequences obtained from ClustalW.

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Additional file 9:

Phylogenic trees showing the relationship between the (A) D and (B) JH sequences. This file contains phylogenic trees for (A) D and (B) JH genes.

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Additional file 10:

Alignment of JH sequences. This file contains a multiple sequence alignment of JH sequences obtained from ClustalW.

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Additional file 11:

Alignment of amino acid VH sequences. This file contains a multiple sequence alignment of amino acid VH sequences obtained from ClustalW. Identical residues are shown as dots (.) and gaps are shown as hyphens (-).

Format: PDF Size: 60KB Download file

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Additional file 12:

Distribution of variable (VH) families in the two IgH loci. Table showing the number of sequences identified per family.

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Additional file 13:

PCR primers and oligo probes. Table listing the PCR primers and oligo probes used in this study.

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