Corporate Banner
Satellite Banner
AgriGenomics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

UC Davis Purchases IRYS System from BioNano Genomics

Published: Tuesday, January 14, 2014
Last Updated: Tuesday, January 14, 2014
Bookmark and Share
The system will advance genome mapping and assembly of wheat relative.


The team of researchers at UC Davis, led by Dr. Jan Dvorak,  will use the Irys System in their workflow as they determine the sequence, location, and orientation of  all genes and transposable elements of the A. tauschii genome.  This information will be used to advance  the assembly and analysis of the wheat genome sequence, which is known to be five times larger and  significantly more complex than the human genome.    

 

“Among the world’s essential crops for human and animal food, the wheat genome has yet to be fully  realized because of its complexity,” said Erik Holmlin, president and CEO of BioNano Genomics. “The UC  Davis  team’s  research  with  A.  tauschii  will  help  determine  how  wheat  genome  is  organized  and  contribute to the large international effort to decode the genome of one of the world’s most important  food crops.”   

 

“To  date,  very  few  highVquality  assemblies  are  available  for  large  and  complex  genomes,  like wheat,  because  we  have  inaccurate,  lowVresolution  physical  maps  on  which  to  arrange  DNA  sequence  information,” stated Han Cao, Ph.D., founder and chief scientific officer of BioNano Genomics. “The Irys  System provides a highVresolution genome map upon which DNA sequences can quickly and accurately  be organized.”   

 

Ancestor Gives Clues to Today’s Wheat    Bread wheat (Triticum aestivum L.) is a hexaploid species containing three different ancestral genomes  (designated A, B, and D), each of which has seven pairs of chromosomes. In addition, approximately 90  percent  of  the wheat  genome  is made up of  repetitive  stretches of DNA, making  the  assembly  of  an  accurate  and  complete  genome map  and  genome  sequence  extremely  difficult.  As  the  progenitor  to  wheat’s D genome,  A.  tauschii  is  a wild grass  that  spontaneously hybridized with cultivated  tetraploid  wheat 8,000 years ago, producing what we know today as bread wheat.   

 

“In order to complete the sequence of a large genome, like that of wheat, we need to know how all the  genes  are organized within each  chromosome  and  the  length  and  location of  the many  long  areas of  repeats,”  said  MingVCheng  Luo,  Ph.D.,  research  geneticist  in  the  Department  of  Plant  Sciences  at UC  Davis and coVPI on the A. tauschii sequencing project. “Despite advances in highVthroughput sequencing,  accurate de novo assembly of a genome has previously been the weak link in genomics research.”       

 

To assemble a genome de novo (from scratch), scientists must determine how the small lengths of DNA  sequences generated from shortVread next generation sequencing (NGS) methods are organized in the  whole  genome.  BioNano’s  Irys  System  is  a  genome  mapping  technology  that  fills  a  void  in  de  novo  assemblies by providing a highVresolution physical genome map to anchor and organize DNA sequence  information to dramatically improve the fidelity of the final genome assembly.        

 

“Last year, we worked with BioNano to generate Irys data that allowed us to quickly create and publish a  highVresolution genome map of a particularly complex region of Aegilops tauschii genome,” said Dr. Luo,  “Based on the success of that collaboration, we have decided to acquire our own Irys system, and we  will  build  upon  that  research  to  create  an  accurate  draft  of  the  entire  D  genome  sequence.  Once  completed, the highVquality draft of A. tauschii D genome can be used by the global research community  to predict gene locations and accelerate genome sequencing and assembly of wheat and its relatives.”   

 

New Technologies Are Reducing the Costs of Genome Research   

 

Assembling a genome  to  completion has  previously been an  intractable  problem because  researchers  have not been able to easily visualize repetitive elements and structural variations. All genomes contain  structural  variations,  which  include  large  sections  of  repeats,  deletions,  duplications,  insertions,  inversions, translocations, and copyVnumber variants.     

 

BioNano’s  Irys  System  is  an  automated,  longVread  technology  that  allows  for  precise  and  accurate  visualization of the underlying organization and structural variation of extended stretches of DNA.   

 

“NGS methods, where the DNA is cut into smaller pieces to be sequenced, loses structural information  making genome assembly an inaccurate, laborVintensive and costly task,” said Dr. Luo. “With BioNano’s  Irys System, we can actually retain the longVrange contiguity of the DNA, which allows us to accurately  assemble  and  finish  genomes  as well  as  compare  the  structural  variations  that  exist among  different  genomes to learn how an organism has genetically adapted to changing environments.”   

 

Dr. Cao added, “The hidden costs in sequencing are assembly, analysis, and annotation of the genome.   Rapid and accurate de novo map assembly with BioNano’s technology makes sequencing projects less  expensive  by  streamlining  the  process  and  providing  a  genome map with  unprecedented  quality  and  accurate  structural  variation  information.   Our  technology  actually  reduces  backend  analysis  costs  so  that  researchers  can  expand  the  number  of  genomes  that  can  be  studied,  thus  supporting  more  comprehensive surveys and comparisons among genomes.”   

 

Safeguarding Wheat’s Future

 

The United Nations has said that harvest yield of wheat will need to increase by 60 percent by 2050 to  meet  the  dietary  needs  for  our  expected  population  growth.  However,  wheat  output  has  recently  plateaued causing alarm in the wheat research and production community. A more complete genomic  map  of wheat  and  ultimately  genome  sequence  could  provide  important  information  on  how wheat  adapts to drought, disease, and temperature changes.   

 

Dr. Luo concluded, “With our recent grant from the National Science Foundation and the integration of  the  Irys  System  and  the  new  highVthroughput V2  chips  into  our workflow, we will  be  able  to  quickly  complete  a highVquality  draft  of  the  A.  tauschii  genome.  By  decoding  the  sequences  of  all  genes  and  determining  their  locations  and  orientations  relative  to  each  other, wheat  geneticists  will  be  able  to  identify changes in the wheat genome that are responsible for the high productivity of modern cultivars.  This knowledge and more efficient breeding techniques based on an accurate wheat genome sequence  will accelerate breeding of new, more productive varieties.”       


Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,400+ scientific posters on ePosters
  • More than 3,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.


Scientific News
New Technique for Mining Health-conferring Soy Compounds
A new procedure devised by U.S. Department of Agriculture (USDA) scientists to extract lunasin from soybean seeds could expedite further studies of this peptide for its cancer-fighting potential and other health benefits.
Rice Disease-Resistance Discovery Closes the Loop for Scientific Integrity
Researchers reveal how disease resistant rice detects and responds to bacterial infections.
Pesticide Found in 70 Percent of Massachusetts’ Honey Samples
New Harvard University study says that the pesticide commonly found in honey samples is implicated in Colony Collapse Disorder.
Oxitec ‘Self-Limiting Gene’ Offers Hope for Controlling Invasive Moth
A new pesticide-free and environmentally-friendly way to control insect pests has moved ahead with the publication of results showing that Oxitec diamondback moths (DBM) with a ‘self-limiting gene’ can dramatically reduce populations of DBM.
More Rice, Less Greenhouse Gas?
An international group from China, Sweden and the U.S. has unveiled a genetically modified super rice that has more starch, yet releases a fraction of the harmful gas methane.
Kiwi Bird Genome Sequenced
The kiwi, national symbol of New Zealand, gives insights into the evolution of nocturnal animals.
Yeast Cells Use Signaling Pathway to Modify Their Genomes
Researchers at the Babraham Institute and Cambridge Systems Biology Centre, University of Cambridge have shown that yeast can modify their genomes to take advantage of an excess of calories in the environment and attain optimal growth.
Faster, Better, Cheaper: a New Method to Generate Extended Data for Genome Assemblies
The Genome Analysis Centre have developed a new library construction method for genome sequencing that can simultaneously construct up to 12 size-selected long mate pair (LMP) or ‘jump’ libraries ranging in sizes from 1.7kb to 18kb with reduced DNA input, time and cost.
New Research Advances Genetic Studies in Wildlife Conservation
‘Next-gen’ DNA sequencing of non-invasively collected hair expands field of conservation genetics.
Fossil Fuel Emissions will Complicate Radiocarbon Dating, Warns Scientist
The paper is published in the journal PNAS.
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,400+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FREE!