Navigation Links
OpGen announces sequence assembly and finishing of first reference genome of domestic goat
Date:12/23/2012

Gaithersburg, Md.December 23, 2012 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," 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."


'/>"/>

Contact: Dan Budwick
dan@purecommunicationsinc.com
973-271-6085
Pure Communications Inc.
Source:Eurekalert

Related biology news :

1. Modern Mobility Aids, Inc. Announces a Revised Agreement for the Acquisition of Lumigene
2. ChromaDex® Announces Financial Results for the Year Ended 2011
3. Improved Authentication and Confidentiality Protection. ICAP Patent Brokerage Announces for Auction Important Patents in Data Encryption and Document Security
4. FirstMark Announces New Hire Jay Houtman as Southeast Regional Sales Manager
5. Global Information Inc. Announces Discounted Conference Registration For Bio-IT World Asia and Biodetection Technologies 2012
6. Virginia Tech announces 2012 football helmet ratings; 2 more added to the 5-star mark
7. Medbox, Inc. Announces Top-Tier Rating by Dun & Bradstreet Credibility Corporation
8. BioLife Solutions Announces 7th Consecutive Quarter of Record Revenue
9. Mass. Eye and Ear announces Curing Kids Fund grant recipients
10. Bay Area PV Consortium announces $7.5 million in grants to lower the cost of large-scale solar
11. BioMed Central announces winners of 6th Annual Research Awards
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:2/10/2016)... , February 10, 2016 ... According to 2016 iris recognition market report, ... recognition is more widely accepted for border ... both fingerprint and iris recognition technology in ... to avoid purchasing two individual biometrics devices. ...
(Date:2/9/2016)... Aware, Inc. (NASDAQ: AWRE ), a leading supplier ... fourth quarter and year ended December 31, 2015.  ... of 2015 was $6.9 million, an increase of 61% compared to ... the fourth quarter of 2015 was $2.6 million compared to $0.2 ... --> --> Higher revenue and operating income in ...
(Date:2/9/2016)... , Feb. 9, 2016 Vigilant Solutions announces today ... reader (LPR) to develop a lead in a difficult homicide ... LPR data to locate the suspect vehicle. Due to the ... case have been omitted at the agency,s request. ... agency explains, "Our victim was found deceased at an intersection ...
Breaking Biology News(10 mins):
(Date:2/10/2016)... ... 2016 , ... LATHAM, NEW YORK... Marktech Optoelectronics will feature their ... in San Francisco’s Moscone Center from February 16-18, 2016, and at the healthcare-focused BiOS ... InGaAs PIN diode standard packages feature a TO-46 metal can with active areas of ...
(Date:2/10/2016)... ... February 10, 2016 , ... SonaCare Medical, LLC reports ... program, Sonalink™ remote monitoring. The inaugural launch of this new technology occurred over ... Dr. Samuel Peretsman to a HIFU technical expert at SonaCare Medical headquarters. ...
(Date:2/10/2016)... ... February 10, 2016 , ... ... a research registry built on the secure online PatientCrossroads platform, has exceeded both ... 1,600 participants have joined the PROMPT study, which seeks to advance understanding of ...
(Date:2/10/2016)... MA (PRWEB) , ... February 10, 2016 , ... ... is now available on Microsoft Azure. On Azure, Arvados provides capabilities for managing ... saw clear demand for Microsoft Azure from major institutions collecting and analyzing genomic ...
Breaking Biology Technology: