Extreme genomic volatility characterises the evolution of the immunoglobulin heavy chain locus in teleost fishes

Abstract

8The evolution of the adaptive immune system has provided vertebrates with a uniquely sophisticated immune 9 toolkit, enabling them to mount precise immune responses against a staggeringly diverse range of antigens. 10 Like other vertebrates, teleost fishes possess a complex and functional adaptive immune system; however, our 11 knowledge of the complex antigen-receptor genes underlying its functionality has been restricted to a small 12 number of experimental and agricultural species, preventing a systematic investigation of how these crucial 13 gene loci evolve. Here, we analyse the genomic structure of the immunoglobulin heavy chain (IGH) gene 14 loci in the cyprinodontiforms, a diverse and important group of teleosts present in many different habitats 15 across the world. We reconstruct the complete IGH loci of the turquoise killifish (Nothobranchius furzeri) 16 and the southern platyfish (Xiphophorus maculatus) and analyse their in vivo gene expression, revealing the 17 presence of species-specific splice isoforms of transmembrane IGHM. We further characterise the IGH constant 18 regions of ten additional cyprinodontiform species, including guppy, amazon molly, mummichog and mangrove 19 killifish. Phylogenetic analysis of these constant regions reveals multiple independent rounds of duplication and 20 deletion of the teleost-specific antibody class IGHZ in the cyprinodontiform lineage, demonstrating the extreme 21 volatility of IGH evolution. Focusing on the cyprinodontiforms as a model taxon for comparative evolutionary 22 immunology, this work provides novel genomic resources for studying adaptive immunity and sheds light on 23 the evolutionary history of the adaptive immune system. 24 29 sequence 1-3 . By combining this enormous diversity in antigen specificities with antigen-dependent clonal 30 expansion and long-term immune memory 4,5 , vertebrates can progressively improve their protection against 31 recurrent immune challenges while also coping effectively with rapidly-evolving pathogenic threats 6 , dramati-32 cally improving their ability to survive and thrive in a complex immune environment.The immunoglobulin heavy chain (IGH) is one of the most important antigen-receptor genes in the adaptive 34 immune system, determining both the effector function and the majority of the antigen-specificity of the anti-35 bodies produced by each B-cell 7,8 . The native structure of the IGH gene locus has a profound effect on adaptive 36 immunity in a species, determining the range of gene segment choices available for the VDJ recombination pro-37 cess giving rise to novel antigen-receptor sequences 2 , the possible antibody classes (or isotypes) available, and 38 the relationship between VDJ recombination and isotype choice 9 . Understanding the structure of this locus is 39 therefore essential for understanding adaptive-immune function in any given vertebrate species, while compar-40 ing loci between species can provide important insight into the adaptive immune system's complex evolutionary 41 Atherinomor...