Free_living_nematodes_from_individuals_to_communities__sequencing_individual_nematode_genomes__metabarcoding_community_diversity_and_BIOSCAN_analysis_of_interaction_ecology-sc-6583
Free_living_nematodes_from_individuals_to_communities__sequencing_individual_nematode_genomes__metabarcoding_community_diversity_and_BIOSCAN_analysis_of_interaction_ecology
This study will generate genomes for individual marine and estuarine free-living nematodes within the Chromadorea and Enoplea. Single worms will be digested to generate long read, linked read and complementary DNA libraries for sequencing. Nematode cuticles (flexible exoskeleton) prevent the implementation of Dr Chris Laumer's novel low input protocol, whereby nuclei are isolated from meiofaunal animals to generate HiC libraries in additon to those listed above.  This research will develop a cuticle disruption pre-treatment step through physical (dounce homogenisation, bead-beating, sonication) or chemical (enzymatic) methods which will break down the cuticle and release nuclei without damage. These nuclei may then be split and permit extraction of sample for Hifi long read genome sequencing, HiC scaffolding and cDNA from a single individual. The development of this method has particular implications for our ability to generate chromosomal assemblies for free-living nematode species which cannot be easily cultured. This project will thus contribute new genome sequences to the Tree of Life, which will contribute to reference libraries to allow the reliable identification of unknown specimens in barcode based sequencing surveys. These genomes will also permit phylogenetic analysis of these species. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
This study will generate genomes for individual marine and estuarine free-living nematodes within the Chromadorea and Enoplea. Single worms will be digested to generate long read, linked read and complementary DNA libraries for sequencing. Nematode cuticles (flexible exoskeleton) prevent the implementation of Dr Chris Laumer's novel low input protocol, whereby nuclei are isolated from meiofaunal animals to generate HiC libraries in additon to those listed above.  This research will develop a cuticle disruption pre-treatment step through physical (dounce homogenisation, bead-beating, sonication) or chemical (enzymatic) methods which will break down the cuticle and release nuclei without damage. These nuclei may then be split and permit extraction of sample for Hifi long read genome sequencing, HiC scaffolding and cDNA from a single individual. The development of this method has particular implications for our ability to generate chromosomal assemblies for free-living nematode species which cannot be easily cultured. This project will thus contribute new genome sequences to the Tree of Life, which will contribute to reference libraries to allow the reliable identification of unknown specimens in barcode based sequencing surveys. These genomes will also permit phylogenetic analysis of these species.