Recombination rate variation and evolution in vertebrates

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PROJECT SUMMARY Meiotic recombination is a fundamental genetic and evolutionary process, initiated by the deliberate infliction of numerous double strand breaks (DSBs) on the genome. In most mammals, these DSBs are specified by PRDM9, which binds DNA through a zinc finger (ZF) array and makes two histone modifications that together serve to recruit the DSB machinery. In these species, the ZF binding affinity is rapidly-evolving. Intriguingly, PRDM9 is not only found in mammals but throughout vertebrates, and may be directing meiotic recombination there too. Despite its broad phylogenetic distribution, the gene has been lost independently many times; in these cases, the determinants of DSB location are less well understood but are associated with promoter features. We propose four analyses that address these gaps in our understanding: Aim 1. Do non-mammalian species with an intact PRDM9 use it to direct recombination? We will test this hypothesis in corn snakes, a vertebrate species that carries a complete and rapidly-evolving PRDM9. We will infer a genetic map from linkage disequilibrium (LD) data as well as by End- seq, a recently-developed approach to assay meiotic DSB frequencies in the genome. We will also collect genomic data about salient histone marks, chromatin accessibility and expression levels. These data will help us to establish if PRDM9 is used to direct recombination. The generality of our findings will be evaluated by building and examining an LD-based map in a fish species with an intact PRDM9, the Northern pike. Aim 2. What mechanisms direct the location of DSBs in species lacking an intact PRDM9? Here, we will focus on two vertebrates: zebra finches, which (like other birds) lack PRDM9 entirely, and swordtail fish, which lack the two N-terminal domains. We will combine existing LD-based genetic maps with data that we will collect on DSB frequencies, salient histone marks, chromatin accessibility, and expression levels. We will then ask which genomic features influence local recombination rates and if they also play a role in species with an intact PRDM9. Aim 3. What genes co-evolve with PRDM9? We will test 246 candidate genes for their co-evolution with PRDM9 across the vertebrate phylogeny. As a byproduct, we will make available a pipeline to identify orthologs of interest. Aim 4. What drives the evolution of PRDM9 binding? To answer this question, we developed a generative model, from PRDM9 binding to population dynamics. We will extend our model, notably to characterize conditions for the loss of PRDM9, and test key predictions with genomic and comparative data. Thus, we will combine population genetic, phylogenetic and experimental approaches in four vertebrate species to learn how DSBs are localized in the genome and how and why the mechanism differs among taxa.