Assembly and annotation of diverse genomes using long-read sequencing technologies

Abstract

The creation of high-quality reference genomes has become increasingly feasible for researchers with the democratization of DNA sequencing brought on by third generation sequencing platforms. New tools are now in the hands of researchers that may have been previously priced out of generating quality genome assemblies. With the steady increase in research groups generating sequence data, the development of rigorous guidelines that are widely applicable across the tree of life are necessary for maximizing the potential of sequence data generated. Here we present a study of simulated sequence data for the model organisms Escherichia coli, Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. We benchmarked several approaches to managing long-read data for de novo genome assembly to develop assembly approach recommendations. From these benchmarks, we created four nematode genomes from strains of C. remanei and C. latens as proof of concept. Additional studies demonstrated the downstream utilization of quality genome assemblies in bacterial isolates that consume acetylene as a primary carbon and energy source. Acetylenotrophy has been documented in a wide range of environmental samples as well as diverse aerobic and anaerobic bacterial isolates. The generation of genomic resources for these isolates allowed for characterization of the organisms, accurate genome-inferred taxonomicplacement and investigation of the metabolic pathways used to transform acetylene. These studies identified the first organisms capable of acetylenotrophic and diazotrophic growth, the anaerobic Syntrophotalea acetylenivorans SFB93T, and the aerobic Bradyrhizobium sp. strain I71. While both capable of consuming acetylene, these studies and others have noted distinct diversity of their causative Acetylene Hydratase enzymes. Further comparison of the genomes of other acetylenotrophs generated in these studies and elsewhere, may give insight into the diversity of this metabolism as well as its evolutionary origin.