WIDESPREAD STRUCTURAL AND CODING SEQUENCE VARIATION HIGHLIGHT RAPID AND ONGOING EVOLUTION OF ZEBRAFISH IMMUNE GENES
Sean McConnell, University of Chicago
Sean C. McConnell1, Kyle M. Hernandez2, Jorge Andrade2, Jill L.O. de Jong1
1. Section of Hematology-Oncology and Stem Cell Transplant, Department of Pediatrics, The University of Chicago, 900 East 57th St, Chicago, IL 60637, USA
2. Center for Research Informatics, The University of Chicago, 5751 S. Woodlawn Avenue, Chicago, IL 60637, USA
Zebrafish excel as a model organism for developmental biology and disease modeling. Traditionally, laboratory zebrafish have been maintained as outbred populations with high genetic variability. Our recent work has examined the core MHC locus in zebrafish, where we found alternative pathways of antigen processing and presentation genes that are separated by 500 million years of evolution. Here we performed highcoverage genomic sequencing for two clonal lines of zebrafish, and one partially inbred zebrafish, to uncover additional sources of immune gene variation throughout these genomes. Pathway analysis identified immune genes as highly enriched among genes under positive selection, or associated with structural variation. Overall, zebrafish genomes are enriched by approximately 5 fold higher levels of variation compared with humans, including SNVs, small indels, and structural variants. Such variation affects additional MHC loci in zebrafish, as well as many other innate immunity genes including the NLR genes. Strikingly, the number of variants present on one arm of zebrafish chromosome 4 (including the bulk of NLR genes, with haplotypic variants covering 10- 20Mb) is nearly what is found in an entire human genome. This disproportionately high variation likely impacts phenotypic traits, particularly those related to immune function. Experimental approaches dependent on known sequences are also highly affected, for example CRISPR/Cas9 gene editing. Genomic sequences for clonal zebrafish lines help to highlight, define, and characterize this rich variation, advancing functional studies in this vertebrate model, and providing insights into the evolution of vertebrate immunity.
Funding: Postdoctoral award from the Chicago Biomedical Consortium (SCM