Plectus is a genus of nematodes known for its exclusive parthenogenesis (asexual reproduction). The general predominance of sexual reproduction in metazoans, despite its significant energetic costs compared to asexual modes, represents a long-standing question in evolutionary biology. While parthenogenesis offers advantages such as rapid replication and independence from mate finding, it is predicted to lead to the accumulation of deleterious mutations and slower adaptation due to the lack of meiotic recombination. However, the frequent occurrence of parthenogenetic taxa in extreme environments suggests adaptive benefits. To further adapt to arduous habitats, Plectus has a remarkable ability to enter cryptobiosis (a state of suspended metabolism also observed in tardigrades and rotifers) to survive desiccation or freezing. This phenomenon is expected to damage the genome sequence and to be only sustainable along accrued DNA repair machineries.
The lack of high-quality genomic resources for Plectus, with only few fragmented genome assemblies previously published, has severely hindered in-depth analysis of how parthenogenesis and cryptobiosis impact their genome structure and evolution in the context of parthenogenesis and cryptobiosis.
CHOPPE first aimed to develop robust methodologies for sequencing and assembling non-model nematode genomes, like Plectus, into collapsed or phased, chromosome-level or highly contiguous sequences. This included utilizing advanced long-read sequencing technologies (PacBio HiFi, Nanopore) and Hi-C reads. Following the application of these methods to several Plectus species, and the closely related sexual species Anaplectus granulosus, the project sought to understand the adaptation and evolution of Plectus, using comparative genomic approaches addressing gene content, repetitive content, and chromosome structure. We additionally aimed to investigate the origin of asexuality in Plectus and test reversal to asexuality. The project also addressed chromosomal adaptations in cryptobiotic nematodes by analyzing chromosome structure conservation in Plectus and Panagrolaimus nematodes, a phylogenetically distant but phenotypically similar cryptobiotic genus.
