Community Research and Development Information Service - CORDIS



Project ID: 617279
Funded under: FP7-IDEAS-ERC
Country: Germany

Periodic Report Summary 2 - EVOLRECOMBADAPT (Recombination in Adaptive Evolution)

The molecular mechanisms that shape genome function during adaptive evolution and species divergence are poorly understood. We aim to explore how meiotic recombination, an essential process of gametogenesis, varies across the genome and among diverging species and influences the distribution of adaptive genetic variation underlying ecological speciation.

We first aim to build individualised, high-resolution genomic maps of recombination cross-overs for marine, freshwater and F1 hybrid stickleback fish. To achieve this we have been whole genome sequencing nuclear families of 2 parents and 94 offspring, whole-chromosome haplotype phasing the data, and using the location of cross-overs in the offspring to build maps of recombination hotspots for both the maternal and paternal individuals (>50% of families complete). Variation in the resulting recombination maps within and among individuals, sexes and species is being studied to elucidate possible genomic features that shape where cross-overs occur (eg DNA sequence motifs) and how genetic variation is shuffled during adaptive divergence. This has involved field collections, development of both methods for high throughput preparation of genomic sequencing libraries and bioinformatic pipelines for phasing and cross-over identification. Preliminary data has revealed considerable variation in recombination across the genome, evidence of recombination "hot-" and "cold-spots" and evidence of specific DNA sequence motifs associated with sex-specific recombination locations.

To supplement this approach with an equally high resolution, higher throughput, but candidate-gene based technique, we have made stickleback-specific antibodies against meiotic proteins involved in DNA doublestranded break (DSB) repair and used these antibodies for chromatin immunoprecipitation followed by sequencing (ChIPseq) of meiotic tissue. This is being used to build maps of genomic locations involved in meiotic DNA double-stranded breaks which may be repaired and resolved as cross-overs or non-crossovers (eg gene conversion). To date we have generated stickleback-specific antibodies for 3 different meiotic proteins involved in DNA DSBs, performed ChIPseq with 2 of these in divergent stickleback ecotypes. We have developed a bioinformatic pipeline in order to compare and contrast ChIPseq peaks (meiotic DSB locations) between divergent stickleback ecotypes and are in the early stages of analysing these results.

Additional aims of our project involve forward genetic mapping to identify the mutations underlying variation and divergence in genomic recombination events between marine and freshwater sticklebacks. A large F2 family has already been generated and we are excited to embrace new technological developments (purchased a new 10x Genomics Chromium linked-read sequencing machine). This is being used to sequence millions of gametes from each of the F2 individuals to identify recombinant molecules and build individualised phenotypic maps of the genomic recombination landscape. The bioinformatic pipeline and linked-read sequencing data are still being developed and will be used to statistically associate (genetically map) cross-over propensity and genomic location with mutations across the genome.

We also aim to used transgenic methods such as cre-lox mediated recombination, to experimentally manipulate recombination and compare the phenotypic effects (eg fitness, survival) of recombinants vs non-recombinants. For this aim, we have been busy optimising crispr transgenic techniques and are in the process of designing and generating the transgenic strains. One of our final aims is to study fitness and survival of recombinants in natural hybrid zone populations using mark-recapture techniques which we have trialled and optimised in the lab. This will be carried out next field season and will provide valuable data on the evolutionary consequences of recombination during ecological speciation in the wild.

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