Analysis of chromosome-level and highly contiguous genome assemblies of Panagrolaimus and Propanagrolaimus

Panagrolaimidae is a widely distributed family of free-living nematodes and includes over 300 documented strains on NCBI Taxonomy. Among these, several species have been shown to survive desiccation and freezing. They can notably be found in extreme environments such as deserts, volcanic islands, Antarctica and the Siberian permafrost. In addition, these worms have various modes of reproduction including hermaphroditism, gonochorism, and a transition to strict parthenogenesis in the genus Panagrolaimus. So far, genomic resources for this family have been scarce. To gain deeper insight into the evolution of Panagrolaimidae from a genomic perspective, we generated chromosome-level and highly contiguous assemblies for Propanagrolaimus and Panagrolaimus species, and a phased assembly for a parthenogenetic Panagrolaimus. Chromosome-level assemblies reveal 5 chromosomes (2n=10) in Propanagrolaimus, and 4 chromosomes (2n=8) in Panagrolaimus resulting from a chromosome fusion. Gene synteny shows large inter and intraspecies rearrangements among Panagrolaimus that are not observed in Propanagrolaimus, and may be linked to DNA strand breaks and repair during cryptobiosis. The phased assembly includes 12 chromosomes, with 4 triplets of homologous chromosomes, confirming the prediction of triploidy in parthenogenetic Panagrolaimus nematodes. Our analysis yields insights into the previously understudied genomic basis for cryptobiosis and parthenogenesis.