No more non-model species: The promise of next generation sequencing for comparative immunology

• Comparative immunologists are facing many challenges that can be solved using NGS.
• NGS will circumvent the need for genome sequences in non-model species.
• NGS can be applied to gene discovery, expression profiling and association studies.
• NGS can be used to study the mechanisms of diversification of immune receptors.
• NGS will reveal the role of epigenetics in immune genes expression and diversity.

Next generation sequencing (NGS) allows for the rapid, comprehensive and cost effective analysis of entire genomes and transcriptomes. NGS provides approaches for immune response gene discovery, profiling gene expression over the course of parasitosis, studying mechanisms of diversification of immune receptors and investigating the role of epigenetic mechanisms in regulating immune gene expression and/or diversification. NGS will allow meaningful comparisons to be made between organisms from different taxa in an effort to understand the selection of diverse strategies for host defence under different environmental pathogen pressures. At the same time, it will reveal the shared and unique components of the immunological toolkit and basic functional aspects that are essential for immune defence throughout the living world. In this review, we argue that NGS will revolutionize our understanding of immune responses throughout the animal kingdom because the depth of information it provides will circumvent the need to concentrate on a few “model” species.