Open Access Research article

Immunoglobulin heavy chains in medaka (Oryzias latipes)

Susana Magadán-Mompó1, Christian Sánchez-Espinel2 and Francisco Gambón-Deza3*

Author Affiliations

1 Oceanographic Center of Vigo, Spanish Institute of Oceanography (IEO), Subida a Radio Faro 50, 36390 Vigo, Pontevedra, Spain

2 Shared Unit of Immunology, University of Vigo - Vigo University Hospital Complex (Hospital Meixoeiro), Edificio de Ciencias Experimentales, Rua das Abeleiras, Campus As LagoasMarcosende, Vigo 36310, Pontevedra, Spain

3 Unidad de Inmunología, Hospital do Meixoeiro, Servizo Galego de Saude (SERGAS), Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain

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BMC Evolutionary Biology 2011, 11:165  doi:10.1186/1471-2148-11-165

Published: 15 June 2011

Additional files

Additional file 1:

List of medaka full length cDNA libraries. The table Table 1S shows all cDNA libraries obtained from different medaka tissues that were analysed to perform this study. The number of cDNA sequences of each library is indicated.

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Additional file 2:

A detailed representation of genomic zone x identified in O. latipes IGH locus. It shows the D, JH segments, constant (C) exons as rectangles or arrowheads. The image displays the location of scaffolds in which these segments were described.

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Additional file 3:

IGH locus with location of the VH genes from G.aculeatus. In this file you can find the G. aculeatus IGH locus sequence with the annotation of the different genic segments. All VH segments present identifiable leader and RSS sequences. This file can be visualized with Vector-NTI program available in http://www.invitrogen.com webcite.

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Additional file 4:

Amino acid sequence alignment of medaka IgM. Alignment is made with the nearest sequences found in Genbank. Canonical cysteines are linked by a line. The first cysteine is marked with an arrow and corresponds to the cysteine required for binding to light chains. Other interesting non-canonical cysteines are also marked with an arrow.

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Additional file 5:

RT-PCR analysis of medaka IgD. Total RNA was obtained from head kidney (HK) and spleen (SP) and RT-PCR was performed using specific primers for Cμ1 and Cδ6. B) IgD domains identification through dot plot of IgD coding cDNA and genomic zone 4 sequence.

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Additional file 6:

Medaka germline nucleotide sequences. In this file you can find nucleotide sequences of different zones described in the medaka IGH locus. The IGHVs file contains the annotation of all VHs. All files can be visualized with Vector-NTI program available in http://www.invitrogen.com webcite.

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Additional file 7:

Phylogenetic trees. This figure show unrooted phylogenetic trees made with domains of O. latipes and G. aculeatus δ left) and μ (right) chains. MEGA4 software, minimum evolution algorithm and JTT matrix were used to draw the tree. Differences by site are activated with gamma parameter 2.5. * The G. aculeatus Cδ5 does not present any orthologous exon in medaka IGH locus.

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Additional file 8:

IGH locus diagram with location of the VH genes from O. latipes. All genes were localized as indicated in material and methods (top left). Alignment of aminoacid sequences deduced from VH genes are at the bottom. The alignment was performed and scored according to recommendations of the IMGT. Naming was done using nomenclature proposed by the same organization. Phylogenetic tree of the VH regions from O. latipes is shown on the top right hand side. MEGA4 software, minimum evolution algorithm and JTT matrix were used to draw the tree. Differences by site are activated with gamma parameter 2.5.

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Additional file 9:

Confirmation of different genomic zones through genomic short reads alignment. This file shows the result obtained after aligning medaka genomic short reads (DRA000220) with the region of zone 1 that presents JH segments and the IGHM gene. Alignment details of short reads with the Cμ1 are indicated. It includes the specific nucleotide sequence to each zone. Identical nucleotides are shown in the same colour (A: green, C: brown, G: lilac, T: blue) and differences are in red and underlined.

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