U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

POPSEQ for Plant Genome Assembly: New Approach Allows Researchers to Work on Many Species Regardless of Sequence Resources
Published: September 02, 2013
Posted: October 23, 2013

Image: Cultivated barley is the fourth most abundant crop in the world and a model for plant genetics research.
(Image courtesy of freefotouk, Flickr CC BY 2.0)

One of the challenges in assembling plant genome “contigs,” fragments of the entire genome that are identified by the assembly algorithms, is that they are not easily linked together or even placed in their proper order. In an effort to mitigate this problem, researchers with the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI) teamed with other researchers to develop another approach for assembling contigs.

In a study published in The Plant Journal, the team reports on the results of testing the approach they call POPSEQ with the barley genome. The plant was selected for DOE JGI’s 2011 Community Sequencing Program portfolio in part for its potential as a bioenergy feedstock crop. Grown on four million acres in the United States, the crop could be used to produce cellulosic ethanol from the straw. More than 80 percent of the 5.1 billion-base genome is composed of repeats, adding to its complexity.

Using POPSEQ, researchers assembled the barley genome while testing a number of variables. For example, they used datasets obtained from different mapping populations, or, in another case, assembled the genome based solely on short reads. The team reported that the results from these tests were comparable with the assembly previously produced by the International Barley Sequencing Consortium. “By comparison,” they wrote, “POPSEQ is inexpensive, rapid, and conceptually simple, the most time-consuming step being the construction of a mapping population…The method is independent of the need for any prior sequence resources,” and this proof of principle demonstrates that POPSEQ can be effectively applied to many species.

Reference: Mascher, M., et al. 2013. “Anchoring and Ordering NGS Contig Assemblies by Population Sequencing (POPSEQ),” The Plant Journal, DOI: 10.1111/tpj.12319. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742, John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Plant Systems and Feedstocks, Plant-Microbe Interactions
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: Computational Biology, Bioinformatics, Modeling

Division: SC-23.2 Biological Systems Science Division, BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Aug 24, 2019
New Approach for Studying How Microbes Influence Their Environment
A diverse group of scientists suggests a common framework and targeting of known microbial processes [more...]

Aug 08, 2019
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures. [more...]

Aug 05, 2019
Amazon Forest Response to CO2 Fertilization Dependent on Plant Phosphorus Acquisition
AmazonFACE Model Intercomparison. The Science Plant growth is dependent on the availabi [more...]

Jul 29, 2019
A Slippery Slope: Soil Carbon Destabilization
Carbon gain or loss depends on the balance between competing biological, chemical, and physical reac [more...]

Jul 15, 2019
Field Evaluation of Gas Analyzers for Measuring Ecosystem Fluxes
How gas analyzer type and correction method impact measured fluxes. The Science A side- [more...]

List all highlights (possible long download time)