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Immunoglobulin light chains in medaka (Oryzias latipes)

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Abstract

The gene segments encoding antibodies have been studied in many capacities and represent some of the best-characterized gene families in traditional animal disease models (mice and humans). To date, multiple immunoglobulin light chain (IgL) isotypes have been found in vertebrates and it is unclear as to which isotypes might be more primordial in nature. Sequence data emerging from an array of fish genome projects is a valuable resource for discerning complex multigene assemblages in this critical branch point of vertebrate phylogeny. Herein, we have analyzed the genomic organization of medaka (Oryzias latipes) IgL gene segments based on recently released genome data. The medaka IgL locus located on chromosome 11 contains at least three clusters of IgL gene segments comprised of multiple gene assemblages of the kappa light chain isotype. These data suggest that medaka IgL gene segments may undergo both intra- and inter-cluster rearrangements as a means to generate additional diversity. Alignments of expressed sequence tags to concordant gene segments which revealed each of the three IgL clusters are expressed. Collectively, these data provide a genomic framework for IgL genes in medaka and indicate that Ig diversity in this species is achieved from at least three distinct chromosomal regions.

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Authors and Affiliations

  1. Virologie et Immunologie Moleculaires, Institut National de la Recherche Agronomique (INRA), Domaine de Vilvert, 78352, Jouy-en-Josas, France

    Susana Magadán-Mompó

  2. Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA

    Anastasia M. Zimmerman

  3. 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

    Christian Sánchez-Espinel

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

    Francisco Gambón-Deza

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  1. Susana Magadán-Mompó
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  2. Anastasia M. Zimmerman
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  3. Christian Sánchez-Espinel
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  4. Francisco Gambón-Deza
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Correspondence to Susana Magadán-Mompó.

Electronic supplementary material

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Supplementary File 1

Table: Medaka full length cDNA libraries. The table includes the number of clones. (PDF 10 kb)

Supplementary File 2

Nucleotide sequences of IGL loci described in the medaka. Individual VLJLCL clusters in medaka IGL1, IGL2, and IGL3 regions, their annotation, and corresponding sequences in a GenBank formats are depicted. (PDF 272 kb)

Supplementary File 3

Phylogenetic analyses of medaka VL segments. An unrooted tree with representative amino acid VL sequences from each VL family and other fish VL sequences constructed using a pairwise deletion algorithm, JTT matrix, and differences by sites activated with gamma parameter 2.5. (PDF 79 kb)

Supplementary File 4

An example of a RSS-J-C coding EST. The alternative translation initiation codon CUG, shown here as CTG, is proposed to precede and open reading frame which originates a J-CL protein. The start codon (CTG) and stop codon (TGA) are shown in red. (PDF 67 kb)

Supplementary File 5

Table: Assignment of VL, JL segments and CL exons in 29 medaka IgL coding ESTs. (PDF 110 kb)

Supplementary File. 6

Analysis of VLJLCL joining in four medaka ESTs (olsp42k18, olsp40b17, olki63m21, and olki48c02). The figure depicts the joining region of alignments of germline VL, JL, CL segments. Although neither N nor P nucleotides were found imprecision in the V-J junction was found suggestive of joining regions contributing to antibody diversity in the medaka model. The four sequences are representative of all 29 ESTs analyzed. (PDF 40 kb)

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Magadán-Mompó, S., Zimmerman, A.M., Sánchez-Espinel, C. et al. Immunoglobulin light chains in medaka (Oryzias latipes). Immunogenetics 65, 387–396 (2013). https://doi.org/10.1007/s00251-013-0678-9

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