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Maryland Scientists Produce High-Quality, Cost-Effective Genome Assembly of Loa loa Roundworm Using SMRT Sequencing

Monday, September 22, 2014

A paper just released in BMC Genomics details what authors call “the most complete filarial
nematode assembly published thus far at a fraction of the cost of previous efforts.” The project was performed using the PacBio® RS II DNA Sequencing System by scientists at the University of Maryland School of Medicine’s Institute for Genome Sciences and the Laboratory of Parasitic Diseases at the National Institute of Allergy and Infectious Diseases.

In this genome sequencing effort, scientists generated a de novo assembly of Loa loa, a roundworm that infects humans. L. loa, transmitted to humans by deer flies, causes loiasis. The parasite lives under the skin and can grow to several centimeters without being detected.

Like other filarial nematodes, the roundworm has proven challenging to grow in labs for in-depth study. Lead author Luke Tallon and his collaborators note that genome sequencing is even more important in such cases since it is a rare opportunity to elucidate the biology of these parasites. The genome they generated with Single Molecule, Real-Time (SMRT®) Sequencing may allow for the development of advanced molecular diagnostics to improve outcomes for patients with nematode infections.

Previous attempts to sequence L. loa were challenged by highly repetitive DNA (it was estimated that 9% of the genome was in repeats) and its AT-rich nature. Tallon et al. tackled a clinical specimen of the organism collected from a patient in the Central African Republic to produce a better assembly. A comparison of short-read sequence data, short- and long-read hybrid data, and long-read-only data found that PacBio data used on its own outperformed other assemblies that included short-read sequence. The final assembly was produced with HGAP2 and polished with Quiver. It includes 96.4 Mbp in 2,250 contigs and covers about 9% more of the genome than a previous draft assembly — in 85% fewer contigs and starting with 80% less DNA, the authors note.

“Recent improvements in long-read, single-molecule sequencing have enabled more economical sequencing and improved genome assembly for previously difficult to sequence clinical samples,” Tallon said in a press release issued by the University of Maryland School of Medicine. “To our knowledge, this study represents the largest and most complete genome of an uncultured clinical specimen successfully sequenced and assembled using this technology.”

Review the full paper, “Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis,” at BMC Genomics.

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