ena-STUDY-LOEWE-TBG-03-08-2020-13:44:48:114-2181
Biodiversity genomics of small metazoa: high quality de novo genomes from single specimens of field-collected and ethanol-preserved springtails
Gold standard genome sequencing relies on large quantities of high quality, high molecular weight (HMW) DNA which is mostly obtained from fresh tissues. The need for high quantities of HMW DNA is problematic for biodiversity genomics: most eukaryotic species are small metazoa which yield minute amounts of DNA. Furthermore, acquisition of fresh materials for DNA extraction is a real challenge for any uncultured minute species and not realistic for the vast majority of them. We overcome those difficulties by sequencing two species of springtails (Collembola) from single specimens preserved in ethanol. We used a newly developed, genome-wide amplification-based protocol to generate PacBio libraries for HiFi long-read sequencing.The assembled genomes were highly continuous. They can be considered complete as we recovered over 95% of Benchmarking Universal Single-Copy Orthologs (BUSCOs). Genome-wide amplification does not seem to bias genome recovery: sequencing a pool of specimens without whole genome amplification recovered a genome with similar completeness. Our study shows that it is possible to obtain high quality genomes from small, field-preserved sub-millimeter metazoans.
Gold standard genome sequencing relies on large quantities of high quality, high molecular weight (HMW) DNA which is mostly obtained from fresh tissues. The need for high quantities of HMW DNA is problematic for biodiversity genomics: most eukaryotic species are small metazoa which yield minute amounts of DNA. Furthermore, acquisition of fresh materials for DNA extraction is a real challenge for any uncultured minute species and not realistic for the vast majority of them. We overcome those difficulties by sequencing two species of springtails (Collembola) from single specimens preserved in ethanol. We used a newly developed, genome-wide amplification-based protocol to generate PacBio libraries for HiFi long-read sequencing.The assembled genomes were highly continuous. They can be considered complete as we recovered over 95% of Benchmarking Universal Single-Copy Orthologs (BUSCOs). Genome-wide amplification does not seem to bias genome recovery: sequencing a pool of specimens without whole genome amplification recovered a genome with similar completeness. Our study shows that it is possible to obtain high quality genomes from small, field-preserved sub-millimeter metazoans.