Conservative evolution of genetic and genomic features inCaenorhabditis becei,an experimentally tractable gonochoristic worm

Caenorhabditisnematodes represent a promising model clade for evolutionary genetics and genomics, but research has focused on the three androdioecious species, those with self-fertile hermaphrodites, all in the Elegans Group of species. The majority ofCaenorhabditisspecies are gonochorists, with males and females, characterized by inconveniently high heterozygosity and inbreeding depression. We have identifiedC. becei,a Japonica Group species from Panamá, as an experimentally tractable gonochorist. We describe a new chromosomal genome assembly of a healthy inbredC. beceireference strain, integrating data from PacBio HiFi reads, Illumina short reads, genetic linkage, and HiC chromatin contacts, and experimental gene annotation with short- and long-read data. Several genetic properties that are well characterized in the Elegans Group are present in this Japonica Group species: the organization of the genetic map, cosegregation of autosomal indels and sex chromosomes, and segregation distortion due to Medea elements, demonstrated here for the first time in a gonochoristicCaenorhabditisspecies. Some aspects of the genome are highly conserved, including synteny across the six chromosomes and the distributions of repetitive sequences and genes along each chromosome. Other features are quite distinctive, including evolved shifts in GC composition & heterogeneity along the genome. Both codon & amino acid usage are shifted in concert with the species' genomic GC content.C. beceihas an unusually large X chromosome, which we find is associated with multiple local gene family expansions. These findings and resources lay the foundation for further experimental and computational studies ofCaenorhabditisgenetics.