Recombination and repetitive genomic landscapes are decoupled in a close relative of Caenorhabditis elegans

Genomes often exhibit heterogeneity across chromosomes, and distributions of protein-coding genes, repetitive elements, and polymorphisms are not uniform along chromosomes in multiple species. One explanation for these patterns is recombination rate variation. As recombination interacts with selection to shape the evolutionary fates of alleles, variation in recombination rate within and between chromosomes could promote differences in the distribution of genomic features across chromosomes. In the nematode Caenorhabditis elegans, recombination rate correlates with multiple genomic features that are non-uniformly distributed along chromosomes. Specifically, in C. elegans, recombination rates are higher on chromosome ends compared to chromosome centers. Its closest known relative, C. inopinata, harbors a radically altered genome with nearly uniform chromosomal distributions of repetitive elements; it likewise has a less heterogeneous chromosomal distribution of polymorphisms and protein-coding genes. Is this dramatic change in genomic organization in any way connected to the evolution of recombination rates? Here, we describe a genetic map of C. inopinata constructed via whole-genome sequencing of 180 individual F2 recombinants. This reveals some chromosomes have a conserved recombination rate domain structure (I, II, III, and X) whereas other chromosomes harbor divergent, more uniform recombination rate distributions (IV and V). Comparisons of these intrachromosomal recombination rates with genomic features (across all autosomes) reveal little covariation between recombination rate, diversity, gene density, and repeat content in C. inopinata (in stark contrast to most Caenorhabditis species). As most autosomes share some conserved recombination domain structure, this suggests that the evolution of recombination may not be entirely responsible for the atypical uniform distribution of repetitive elements across C. inopinata chromosomes. Taken together, these observations reveal that recombination rates can be decoupled from the chromosome-level organization of repetitive elements.