Genetic maps improve the reference genome assembly of the candidate bioenergy feedstock
The Science:
A team of French researchers developed an array that allowed them to produce high-resolution genetic maps of two eucalyptus species that they then compared to the reference genome of eucalyptus produced by a team including DOE JGI researchers.
In a report published earlier this year, the eucalyptus genome was found to have more than 36,000 genes. Bioenergy researchers are interested in the genes involved in the production of plant cell wall material. (Image courtesy of the University of Pretoria.)
The Impact:
The genetic maps have allowed DOE JGI researchers to improve the reference genome assembly of eucalyptus, available on the plant portal Phytozome.
Summary
Cartographers create maps that show people where to find buildings, cities, or even whole countries, and how these landmarks are situated in relation to each other. For geneticists, a genetic map performs a similar task, linking a gene to a particular trait or condition. These maps also help researchers figure out what chromosome the gene is on, where in the chromosome this gene resides, and can help suggest a gene’s function(s).
In a study that appeared online November 10, 2014 in New Phytologist, a team that included Jeremy Schmutz, Plant Program Head at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, reported the development of two genetic maps that improve the genome assembly of eucalyptus. Grown on 40 million acres in 100 countries, the DOE considers fast-growing and oil-rich eucalyptus a candidate biomass energy crop and sequenced its genome under the DOE JGI Community Science Program. Schmutz was also part of the team that first described the Eucalyptus grandis genome of a Brazilian tree (BRASUZ1) in a Nature paper published this past June.
In this study, French researchers conducted whole-genome resequencing of two eucalyptus species, E. urophylla and E. grandis. Using the DNA sequence variants or SNPs found in the E. grandis genome sequence published by the DOE JGI-led team back in June, the researchers then designed a high-quality SNP DNA-based genotyping array that allowed them to link genes to chromosomes.
“In our study the use of two independent and highly collinear genetic maps enabled cross-validation in the comparison between the genetic maps and the reference genome sequence,” the team reported. In comparing their findings to the BRASUZ1 reference genome, they found 41 potential false joins on two chromosomes, and were able to localize a few million bases of sequence to another seven chromosomes. These findings ultimately helped improve the E. grandis genome assembly available on the DOE JGI plant portal Phytozome, which, in turn, will improve the usefulness of the eucalyptus sequence for bioenergy studies.
Contact
Jeremy Schmutz
DOE Joint Genome Institute Plant Program Head
HudsonAlpha Institute for Biotechnology
jschmutz@husdonalpha.org
Funding
- U.S. Department of Energy Office of Science
- FEDER
- ERANET Plant KBBE
Publication
- Bartholomé J et al. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol. 2014 Nov 10. doi: 10.1111/nph.13150. [Epub ahead of print]