New approach allows researchers to work on many species regardless of sequence resources
The Science
Plant genomics researchers evaluated POPSEQ, a method for assembling complex plant genomes using next-generation sequencing.
The Impact
Using a large, complex and highly-repetitive plant genome, the findings yielded results comparable to the previously assembled sequence. The proof of principle demonstrates that POPSEQ is a low-cost, rapid and effective assembly method that can be applied to many species.
Summary
Cultivated barley is the fourth most abundant crop in the world and a model for plant genetics research.
During the this year’s Genomics of Energy & Environment Meeting, DOE Joint Genome Institute Plant Program head Jeremy Schmutz reminded the audience that, “Plant genomes are hard because of polyploidy and polymorphisms and … repeat content and transposons. But we care about them because these are the mechanisms that drive plant evolution.” One of the challenges in assembling plant genomes is that whole-genome sequencing doesn’t allow researches to easily link contigs or identify the linear order along chromosomes. In an effort to mitigate this problem, Schmutz and other DOE JGI colleagues teamed with researchers to develop another approach to assemble contigs.
In the study published September 2, 2013 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 the 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 million-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 results from these tests, reported the team, 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 will enable the rapid and cost efficient establishment of powerful genomic information for many species.”
Contacts
Nils Stein
Leibniz Institute of Plant Genetics and Corp Plant Research, Germany
stein@ipk-gatersleben.de
Robbie Waugh
The James Hutton Institute, UK & University of Dundee, UK
robbie.waugh@hutton.ac.uk or r.waugh@dundee.ac.uk
Funding
- DOE Office of Science, Office of Biological and Environmental Research
- Triticeae Coordinated Agricultural Project, USDA-NIFA
- Scottish Government Rural and Environmental Science and Analytical Services Division Research
- German Ministry of Research and Education
Publications
- Mascher M et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 2013 Sep 2. doi: 10.1111/tpj.12319. [Epub ahead of print]