Going the Long (Molecule) Way: Detecting Structural Features Influencing Recombination Rate via SMRT-Seq and Optical Mapping in the Crow Genome

Accurate and contiguous genome assembly is key to a understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture it is associated with centromeric and telomeric regions and influences meiotic recombination. Here we assess the impact of large tandem repeat arrays on the recombination rate landscape in the Eurasian crow. We assembled two genome references using single-molecule real-time (SMRT) sequencing and single-molecule optical maps. A three-way comparison including the published short-read assembly constructed for the same individual allowed assessing assembly properties and pinpointing mis-assemblies. We characterized 36 previously unidentified large repetitive regions at sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. We estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. Our findings are consistent with an effect of low recombination in regions adjacent to centromeric or sub-telomeric heterochromatin, and add to our understanding of the processes generating genetic diversity. By combining three independent technologies, our results highlight the importance of adding a layer of information on genome structure inaccessible to each approach independently.