Low_input_approaches_to_generate_high_quality_reference_genomes_for_parasitic_flatworms-sc-6197
Low_input_approaches_to_generate_high_quality_reference_genomes_for_parasitic_flatworms
The study is intended to cover the gene annotation (RNA sequencing) portion of the 'Low-input approaches to generate high-quality reference genomes for parasitic flatworms'  project (abstract below).   The RNA sequencing will consist of NovaSeq (1 lane, ~50 samples, aiming for > 50 million reads per sample (multiple samples per species)) and PacBio Iso-Seq ~22 samples. These will assist in the production of high quality gene models for 15 trematode species (mostly schistosoma) for which we already have chromosomal reference genomes (produced as part of another project by db22).  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/
Hundreds of millions of people worldwide are infected with one or more species of parasitic flatworm. These infections typically cause chronic, debilitating infections resulting in substantial social and economic burdens. While efforts to understand and control these infections are ongoing, there is still a lack of high-quality, annotated reference genomes for many of these species. As a result, key questions about the biology and epidemiology of these species go unanswered. For example, within the genus Schistosoma only one species, Schistosoma mansoni, has a reference genome of chromosomal contiguity and completeness despite the fact that humans are the definitive host for at least seven Schistosoma species.   In an effort to increase the quality and range of genomic resources available we have used a combination of low-DNA input PacBio sequencing and long-range scaffolding approaches (Chromium Linked-Reads and Arima Hi-C) to generate de novo genome assemblies using unamplified DNA from single trematode isolates. This has allowed us to circumvent the high DNA input requirements of most sequencing technologies and include highly diverse and outbred species. Using this approach, we have generated chromosomal-scale reference-quality genome assemblies for 12 trematode species, primarily from Schistosoma. We aim to combine these assemblies with full-length cDNA (PacBio Iso-Seq) sequencing to produce high-quality gene annotations. We will demonstrate the utility of this dataset by performing a phylum-wide analysis of Platyhelminthes which revealed substantial variation in both genome size and gene content. These data will represent a high-quality resource for understanding the evolution of Platyhelminthes accelerating our understanding of their biology and epidemiology as they are targeted for control.