OpGen, Inc. today announced its ARGUS® Whole Genome Mapping System technology was used in combination with next-generation sequencing (NGS) to produce the first, high-quality reference genome of the domestic goat. The study, which was led by BGI-Shenzhen and Kunming Institute of Zoology, Chinese Academy of Sciences was published online today in Nature Biotechnology. The paper, titled Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus), demonstrates the value, efficiency and cost effectiveness of OpGen's Whole Genome Mapping in de novo assemblies of large, complex genomes.
“This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing”
"This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing," said Xun Xu, Deputy Director, BGI-Shenzhen. "The experience in these genome assembly projects shows that the physical whole genome map should be the standard for any reference genome to be assembled in the future."
Goats are an important economic resource in many developing countries around the globe, including China and India. However, despite their agricultural and biological importance, breeding and genetic studies of goats have been hindered by the lack of a high-quality reference genome sequence. The goat genome is the first high-quality reference genome for small ruminate animals and may help to advance the understanding of distinct ruminant genomic features from non-ruminant species.
Although generating draft assemblies from NGS is relatively easy, finishing a sequence to the chromosome level is still difficult and costly. The findings show that a single NGS platform, when combined with Whole Genome Mapping, can produce a finished assembly much faster and less expensively than other currently available mapping strategies such as bacterial artificial chromosome (BACs) or fluorescence in situ hybridization (FISH). This approach sets the gold standard in large genome de novo assembly, eliminating the need for genetic maps which can be very time consuming.
"By incorporating Whole Genome Mapping, we were able to overcome the limitations of NGS' short read scaffolds to produce long super-scaffolds and finish the assembly to the near chromosome level," said Wen Wang, Deputy Director, Kunming Institute of Zoology, Chinese Academy of Sciences and an author of the paper. "We could not have completed the project without OpGen's technology."
In the study, OpGen's ARGUS system produced 100,000 single molecule restriction maps in three hours. This resulted in 30 times the physical coverage of the goat genome. The company's Genome Builder™ software generated long super-scaffolds by combining single molecule map data with sequence scaffolds generated by NGS and subsequent assembly. Specifically, the metric of assembly (N50) was improved eightfold by combining Whole Genome Mapping with NGS over NGS alone.
"While we continue to demonstrate the value of Whole Genome Mapping for assembly, quality control and validation of microbial genomes, we are pleased to expand its applications as a critical, complementary technology enabling investigators to provide complete and accurate long-range genomic information in complex, de novo projects," said Richard Moore, M.D., Ph.D., chief scientific officer of OpGen and an author of the paper. "This paper is the first of many we expect to be published over the next year which will validate OpGen's Whole Genome Mapping technology as a solution for the de novo assembly of the spectrum of genomes from microbes to mammals."
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