Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus

The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicated virtually all genomic analyses. Here, we present a de novo genome assembly from single-molecule, long-read sequencing data consisting of 135 P. pacificus contigs. When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes. This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P. pacificus. Despite widespread conservation of synteny between P. pacificus and C. elegans, we identified one major translocation from an autosome to the sex chromosome in the lineage leading to C. elegans. This highlights the potential of the chromosome-scale assembly for future genomic studies of P. pacificus. [Display omitted] •Highly contiguous assembly based on single-molecule sequencing data•99% of the assembly is ordered and oriented into six chromosomes•Linkage disequilibrium and macrosynteny support chromosome structure•One major interchromosomal translocation along the C. elegans lineage The nematode Caenorhabditis elegans is one of the most attractive animal systems available to study basic biological processes. Rödelsperger et al. present a chromosome-scale genome assembly of the related Pristionchus pacificus as a resource for studying developmental systems drift, the genetics of phenotypic plasticity, and genome evolution.