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

Genomes exhibit chromosomal heterogeneity. Distributions of 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, recombination rate variation could promote differences in the chromosomal distribution of genomic features. Thus, clarifying the relationship between recombination rates and genomic organization is a major goal of genetics. In the nematode Caenorhabditis elegans , recombination rate correlates with multiple genomic features that are non-uniformly distributed along chromosomes; recombination rates and repeats 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. Is this dramatic change in genomic organization connected to the evolution of recombination rates? Here, we describe a genetic map of C. inopinata constructed via whole-genome sequencing of 180 individual F ₂ recombinants. This reveals four chromosomes have a conserved recombination rate domain structure whereas two other chromosomes harbor divergent, more uniform recombination rate distributions. Comparisons of these intrachromosomal recombination rates with genomic features reveal little covariation between recombination rate, diversity, gene density, and repeat content in C. inopinata (in stark contrast to most Caenorhabditis species). 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 genomic organization of repetitive elements.