Abstract
A high quality genome assembly is a vital first step for the study of an organism. Recent advances in technology have made the creation of high quality chromosome scale assemblies feasible and low cost. However, the amount of input DNA needed for an assembly project can be a limiting factor for small organisms or precious samples. Here we demonstrate the feasibility of creating a chromosome scale assembly using a hybrid method for a low input sample, a single outbred Drosophila melanogaster. Our approach combines an Illumina shotgun library, Oxford nanopore long reads, and chromosome conformation capture for long range scaffolding. This single fly genome assembly has a N50 of 26 Mb, a length that encompasses entire chromosome arms, contains 95% of expected single copy orthologs, and a nearly complete assembly of this individual's Wolbachia endosymbiont. The methods described here enable the accurate and complete assembly of genomes from small, field collected organisms as well as precious clinical samples.
Highlights
The creation of high quality genome assemblies is a key step for the study of organisms on both the level of individuals and populations [1]
While short reads can be reassembled into larger contiguous genome segments by identifying overlapping reads, they often fail to generate chromosome length assemblies due to the challenge of assembling repetitive DNA sequences
High molecular weight DNA was extracted from one half of a single D. melanogaster female using a Qiagen MagAttract high molecular weight (HMW) DNA kit
Summary
The creation of high quality genome assemblies is a key step for the study of organisms on both the level of individuals and populations [1]. Conventional genome sequencing projects rely on whole-genome shotgun sequencing approaches that generate huge numbers of short sequence reads at low cost. While short reads can be reassembled into larger contiguous genome segments by identifying overlapping reads, they often fail to generate chromosome length assemblies due to the challenge of assembling repetitive DNA sequences. Fragmented genomes can be valuable for gene-level studies but many genomic analyses such as understanding chromosome-scale evolution, resolving full-length haplotypes, association studies, and quantitative trait locus mapping require high-quality chromosome-scale assemblies. New hybrid genome assembly approaches can produce highly contiguous assemblies that represent true chromosome length genomes [3]
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