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UC Davis Purchases IRYS System from BioNano Genomics

Published: Tuesday, January 14, 2014
Last Updated: Tuesday, January 14, 2014
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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.”       

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