There is plenty of buzz out there for the big data biology projects–but usually the focus is the human data (with a few token model organisms thrown in). But this week plant researchers renewed the call for big plant data. I’m totally on board with that.
The 1000 Genomes project to obtain more human variation information is well underway, funded, and has companies supporting it. And that’s great–I’m all for this too! But as someone who survives largely on the kindness of plants I want more plant research going on. I want to see this funded and supported. And as we face increasing stresses on resources from limitations like oil and water supplies to wacky climate conditions and environmental consequences I think we could well afford to spend less time gazing at our human genomic navels and devote more attention to the plants.
There is already some work on this Arabidopsis project. The first paper with data on this effort came out last fall. But the researchers are still having to go out and lobby for this project. A new opinion piece in Genome Biology calls out for awareness and support for this effort.
They have already done a first generation green HapMap. The paper last fall illustrated the feasibility of the project by looking at the reference Col-O (Columbia) and Bur-O and Tsu-1 strains. The paper presents the process, compares their pipeline software with another package (SHORE that they developed and MAQ), They have a GBrowse installation that presents the data (and you can get free training on GBrowse here to effectively use the site). They also provide data to TAIR.
I think this is important and I hope it gets the same level of support and respect that 1000 humans will get.
1001 Genomes main site: http://1001genomes.org/
1001 Genomes GBrowse: http://gbrowse.weigelworld.org/cgi-bin/gbrowse/ath_reseq_1001/
Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Scholkopf, B., Nordborg, M., Ratsch, G., Ecker, J., & Weigel, D. (2007). Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana Science, 317 (5836), 338-342 DOI: 10.1126/science.1138632
Ossowski, S., Schneeberger, K., Clark, R., Lanz, C., Warthmann, N., & Weigel, D. (2008). Sequencing of natural strains of Arabidopsis thaliana with short reads Genome Research, 18 (12), 2024-2033 DOI: 10.1101/gr.080200.108
Weigel, D., & Mott, R. (2009). The 1001 Genomes Project for Arabidopsis thaliana Genome Biology, 10 (5) DOI: 10.1186/gb-2009-10-5-107