Strawberries, Chocolate and Open Access Genomics
Nature Genetics seems to have taken a page from the Food Network Magazine by timing two publications to the annual obsession with festive foods among many, NG readership included. I am talking about the genomes of the Strawberry and of the Cocoa plants. Both are important crops, both are components of luxurious eating. Both papers are comprehensive reports, which give no immediate new insights into the biology of either plant but whose data can be hopefully used later to the advantage of crop growers.
One thing I learned form the Cocoa paper: Cocoa may be a recent descendant of the common eudicot ancestor, and becuase of that and because it is easily manipulated, it can bee a good model for tree fruit crops.
It does not, however, boost immunity:
Two things I learned from the Strawberry paper: strawberries have small genomes. Seven chromosomes, diploid, 240,000,000 bp. The smallest plant genome sequenced so far, besides Arabidopsis thaliana. They actually managed to do it all with de-novo assembly from short reads. Wow.
But the other very important thing I learned is that the strawberry project had no central funding source, and that the genome sequencing and assembly were done under an open-access model. Now that is actually cool and interesting. I looked a bit on the web, trying to find how this project was managed, but I only came up with university press releases and this server. I would be really interested to read a methods paper on how to manage a community-based open-access genome project. Publishing their methodology would have a serious benefit to the genomics community.
UPDATE: Kevin Folta has shared the story behind the story of the strawberry genome. A great read about politics, plants, papers and punding… er.. funding.
Based on image from Clockworkgrue, Flickr
Argout, X., Salse, J., Aury, J., Guiltinan, M., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S., Abrouk, M., Murat, F., Fouet, O., Poulain, J., Ruiz, M., Roguet, Y., Rodier-Goud, M., Barbosa-Neto, J., Sabot, F., Kudrna, D., Ammiraju, J., Schuster, S., Carlson, J., Sallet, E., Schiex, T., Dievart, A., Kramer, M., Gelley, L., Shi, Z., Bérard, A., Viot, C., Boccara, M., Risterucci, A., Guignon, V., Sabau, X., Axtell, M., Ma, Z., Zhang, Y., Brown, S., Bourge, M., Golser, W., Song, X., Clement, D., Rivallan, R., Tahi, M., Akaza, J., Pitollat, B., Gramacho, K., D’Hont, A., Brunel, D., Infante, D., Kebe, I., Costet, P., Wing, R., McCombie, W., Guiderdoni, E., Quetier, F., Panaud, O., Wincker, P., Bocs, S., & Lanaud, C. (2010). The genome of Theobroma cacao Nature Genetics DOI: 10.1038/ng.736
Shulaev, V., Sargent, D., Crowhurst, R., Mockler, T., Folkerts, O., Delcher, A., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S., Burns, P., Davis, T., Slovin, J., Bassil, N., Hellens, R., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O., Jensen, R., Allan, A., Michael, T., Setubal, J., Celton, J., Rees, D., Williams, K., Holt, S., Rojas, J., Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S., Troggio, M., Viola, R., Ashman, T., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H., Bryant, D., Fox, S., Givan, S., Wilhelm, L., Naithani, S., Christoffels, A., Salama, D., Carter, J., Girona, E., Zdepski, A., Wang, W., Kerstetter, R., Schwab, W., Korban, S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J., Salzberg, S., Dickerman, A., Velasco, R., Borodovsky, M., Veilleux, R., & Folta, K. (2010). The genome of woodland strawberry (Fragaria vesca) Nature Genetics DOI: 10.1038/ng.740
So, we have the genome for wheat, now strawberry.
I guess it’s time to get a chocolate biscuit/cookie tree, or chocolate dipped strawberry bush.
I second the call for a methods paper on how to organize a genome project without a central grant and the hierarchy that comes with it.
@Dave Gilbert
We do not, in fact, have the genome for wheat. At >10 GB, the genome of wheat is over fifty times the size of strawberry, consists of three closely related homoeologous sets of chromosomes and is loaded with so much repetitive sequence it makes the genome of CORN look simple.