T2T genomes of <i>Caenorhabditis nigoni</i> and <i>Caenorhabditis briggsae</i> reveals extensive loss of satellite DNA associated with self-fertilization

The two closely related <i>Caenorhabditis</i> nematode species, <i>C. nigoni</i> and <i>C. briggsae</i> , are commonly used to study the evolution of reproductive modes in animals, with the self-fertile <i>C. briggsae</i> and outcrossing <i>C. nigoni</i> sharing a common ancestor ∼3.5 million years ago. Earlier genomic analyses of these species revealed genome shrinkage associated with selfing and proposed that at least some gene loss can be adaptive. However, the incomplete <i>C. nigoni</i> reference genome limited most comparative analyses to genic regions. Here, we leveraged long-read sequencing to generate a telomere-to-telomere (T2T) assembly for the <i>C. nigoni</i> strain JU1422 and the <i>C. briggsae</i> strain AF16. This new 139Mb <i>C. nigoni</i> genome resolved 57 gaps and 149 unassigned scaffolds from the previous genome assembly. Comparison with the 107Mb T2T <i>C. briggsae</i> genome reveals that the major driver of genome content differences are deletions to satellite DNA arrays, reflecting a loss of 9.6Mb. Interestingly, many of the differences are on the <i>C. nigoni</i> X chromosome, which is >13Mb larger than in the previous assembly. The transition to selfing was thus accompanied by a 37% reduction in the size of the sex chromosome compared to 16-21% shrinkage of the autosomes. We also document a surprising degree of plasticity in the ribosomal DNA, with the X chromosome harboring a second 45S rDNA array that is absent in <i>C. briggsae</i> . Our analysis reveals that obligatory outcrossing may play a major role in the maintenance of satellite DNA arrays.