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An Illumina approach to MHC typing of Atlantic salmon

  • Arvind Y. M. Sundaram
  • Åse Helen Garseth
  • Giuseppe Maccari
  • Unni GrimholtEmail author
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Part of the following topical collections:
  1. Nomenclature, databases and bioinformatics in Immunogenetics

Abstract

The IPD-MHC Database represents the official repository for non-human major histocompatibility complex (MHC) sequences, overseen and supported by the Comparative MHC Nomenclature Committee, providing access to curated MHC data and associated analysis tools. IPD-MHC gathers allelic MHC class I and class II sequences from classical and non-classical MHC loci from various non-human animals including pets, farmed and experimental model animals. So far, Atlantic salmon and rainbow trout are the only teleost fish species with MHC class I and class II sequences present. For the remaining teleost or ray-finned species, data on alleles originating from given classical locus is scarce hampering their inclusion in the database. However, a fast expansion of sequenced genomes opens for identification of classical loci where high-throughput sequencing (HTS) will enable typing of allelic variants in a variety of new teleost or ray-finned species. HTS also opens for large-scale studies of salmonid MHC diversity challenging the current database nomenclature and analysis tools. Here we establish an Illumina approach to identify allelic MHC diversity in Atlantic salmon, using animals from an endangered wild population, and alter the salmonid MHC nomenclature to accommodate the expected sequence expansions.

Keywords

MHC Illumina IPD-MHC database Nomenclature Salmonid Atlantic salmon 
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Notes

Acknowledgements

We thank Randi Faller at the Norwegian Veterinary Institute for excellent technical assistance.

Author contribution

Study was conceptualised by UG, ÅHG and AYMS. AYMS along with UG designed the primers used in library preparation and analysed the sequence data. AYMS wrote the custom scripts with assistance from GM. Library preparation and optimisation were performed by UG. Results were further analysed and interpreted by UG with assistance from AS. Nomenclature was changed by GM and UG. All authors contributed to writing the manuscript.

Funding information

This study was funded by the strategic institute projects “BioDirect” and “Seq-Tech” at the Norwegian Veterinary Institute and the Norwegian Research Council project no. 274635. ÅHG is supported by funding from the Norwegian Environment Agency. GM is supported by funding from the UKRI-BBSRC award BB/M011488/1. Sequencing was performed at Norwegian Sequencing Centre, Ulevål, Oslo, Norway. 

Supplementary material

251_2019_1143_MOESM1_ESM.pdf (726 kb)
Supplementary file 1. New IPD-MHC Fish nomenclature (PDF 725 kb)
251_2019_1143_MOESM2_ESM.pdf (518 kb)
Supplementary file 2. Illumina Statistics (PDF 518 kb)
251_2019_1143_MOESM3_ESM.pdf (589 kb)
Supplementary file 3. MHC sequences (PDF 589 kb)
251_2019_1143_MOESM4_ESM.pdf (543 kb)
Supplementary file 4. UBA primer regions (PDF 543 kb)
251_2019_1143_MOESM5_ESM.pdf (1.3 mb)
Supplementary file 5. MHC sequence alignments (PDF 1303 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Norwegian Veterinary InstituteOsloNorway
  2. 2.Department of Medical GeneticsOslo University HospitalOsloNorway
  3. 3.The Pirbright InstituteWokingUK
  4. 4.Anthony Nolan Research InstituteLondonUK

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