[
International Worm Meeting,
2021]
Nematodes are one of the most abundant phyla in the animal kingdom. Along with Caenorhabditis elegans, several other soil nematodes and some parasitic species have been established as laboratory model organisms. For these species well-annotated and high-quality reference genomes have been established. Usually a huge number of animals are pooled to generate libraries for sequencing resulting in a final genome sequence of the species. However, the information about the diversity within the species is usually lost and only a fraction of nematode species can be cultivated and studied in laboratories. Small size and cryptic anatomical features makes the isolation of sufficient nematodes of the same species within a meiofaunal community extremely difficult. We are developing a low-input method for generating high-quality annotated genomes and can generate long-read HiFi genomic DNA libraries and transcriptome libraries from a single isolated nematode. We are working towards also generating Hi-C chromatin conformation capture libraries and linked-read genomic libraries for single individuals. Initial studies using single individuals of the soft-bodied flatworm Stenostomum confirmed that preparing all four libraries from single animals is indeed achievable, despite the limited number of cells. We optimised different tissue disruption methods to recover intact nuclei from individual animals. With these intact nuclei in suspension we can isolate RNA, high molecular weight DNA and take a fraction of the nuclei for Hi-C library preparation. Through optimizing the extraction protocol and different library preparation steps we will be able to gain sequencing data of long-read, proximity-read, linked-read and transcriptome sequencing which will provide us with a high-quality genome. Thus, it will be possible to explore the genomic diversity within populations, among populations and across species at the resolution of single individuals. Further, this low-input method will be of great benefit for identifying and studying these and other meiofaunal species, and understanding the ecology of their communities.
[
International Worm Meeting,
2021]
Chromosome diminution involves specific deletion of parts of the germline genome from somatic cells. This phenomenon, first described in ascaridid nematodes, has been found widely (in protists, plants and animals), but occurs sporadically within any given clade. Using long read genome sequencing we identified chromosome diminution in the rhabditine nematode Oscheius tipulae, where this phenomenon had not been reported before. Many kilobases of DNA are removed from each end of every chromosome, including deletion of expressed genes, and new telomeres synthesized (see https://doi.org/10.1093/g3journal/jkaa020). By long-read sequencing of additional species we have identified similar patterns of diminution across the genus Oscheius - deletion of subtelomeric sequence and addition of new telomeres. Using these sequences we have explored the genomic contexts of diminution and begun to test hypotheses of the mechanism and functions of diminution. Long read sequencing has changed our understanding of Oscheius genomes, and we wonder if diminution processes may be more widely distributed.