September 1, 2011
Mapping a model: Researchers' international collaboration to sequence, analyze genome of plant species appears in journal Nature
Two Kansas State University researchers have been collaborating on an international project involving genomes of a model plant species that can offer insights into other plants.
Christopher Toomajian, assistant professor of plant pathology, and Katie Hildebrand, doctoral student in plant pathology, Stafford, are researching genetic variation in Arabidopsis thaliana, a small flowering plant that has a short life cycle, making it one of the best model species for scientific study.
For some of their latest research, they have worked with researchers from the University of Utah, the United Kingdom and Germany. Their collaborative work, titled "Multiple reference genomes and transcriptomes for Arabidopsis thaliana," appears online in the journal Nature and focuses on the sequencing and analysis of Arabidopsis genomes.
By knowing the genetic makeup of a model species like Arabidopsis, researchers can better understand how other plants work and behave.
"It's part of a much greater understanding of how genomes function in plants and the relevance of differences in individuals of the same species," Toomajian said.
The article is twofold: It includes data from the United Kingdom researchers who have sequenced 18 genomes of Arabidopsis. But it also includes analysis from the other groups, including the K-State researchers, who looked at transcription data -- data that shows where in the genome DNA is converted into RNA so that it can be expressed as a functional protein in the plant.
The genome for Arabidopsis thaliana was sequenced in 2000, making it the first plant to have its genome sequenced.
"People working with Arabidopsis have been way ahead of the game in the sense that we have had, at least for one individual plant, the whole genome for more than 10 years and we have been able to predict most of the genes and proteins that it codes for," Toomajian said. "What people have been doing in recent years is moving beyond just a single genome sequence, since one reference sequence can't accurately predict the consequences of all of the variations that you would find within a species."
Part of the research featured in the Nature article was the result of an ongoing National Science Foundation grant worth more than $700,000. Toomajian is a co-principal investigator along with University of Utah researcher Richard Clark. Hildebrand is helping with the research.
"I've always been interested in genetics as well as variation and expression, so I found this project very exciting," Hildebrand said.
As part of the project, Clark collects gene expression data from Arabidopsis plants and sends it to the group of Gunnar Ratsch at the Friedrich Miescher Laboratory of the Max Planck Society in Germany for analysis. Toomajian and Hildebrand have participated in the analysis of genome sequence data from collaborator Richard Mott, a researcher with the Wellcome Trust Centre for Human Genetics at the University of Oxford. The K-State researchers have also worked to compare sequence variation data with the analyzed gene expression data.
Their work so far involving Arabidopsis seedlings is what appears in the Nature article. They now want to obtain similar gene expression data from Arabidopsis floral buds and roots so they can understand variation in gene expression in different plant tissues. Ultimately the team wants to see if gene expression patterns specific to different stages of plant growth, from seedlings to flowers and roots, are also variable within the species.
"People have started to realize that the differences within a species or changes that occur between species are often a lot more than just changes in protein sequences," Toomajian said. "Timing of these genes can also lead to lots of important functional changes in how the plants work and behave. We're trying to get to the bottom of the relevance of some of these differences in gene expression in a good model plant species."