Video Tip of the Week: Phytozome and the Peach Genome

peaches

We’ve laughed in the past about a “genome of the day” because there are so many projects each week that we want to explore, and it’s hard to keep up. But recently I wanted to have a look at the peach genome project, because–well, peaches!

And the summary papers are nice. But generally I want to look around that the resources that are now available for exploring that draft genome. So in the paper the team provides links to a number of places where you can go beyond what’s published and further analyze the outcomes.

You can see the peach genome data and tools available at GDR, the Genome Database of Rosaceae. They’ve got a number of tools, including an installation of GBrowse for graphically browsing the genome. But they also have a neat synteny view of strawberry-peach-apple. I never had a software tool that made me crave a frosty smoothie before… They have additional resources at the GDR site that span quite a range of users–there’s a set of Breeders Toolbox options that you never see with mammalian genomes–ya know?

Another site that you can explore for more details about the peach genome data is Phytozome. In this week’s video tip I examine some of the tools you can use at Phytozome to explore the peach genomic data, but you’ll find other genomes are accessible from the site as well. Calculated gene family relationships can be examined among the species with various viewer and sequence tools.

In the video I explore some of the basic browsing options, but I don’t have time to cover some of the other great features at Phytozome. So I encourage you to check out their paper that explains more about how they organize their data, the additional calculations of the gene family relationships, and the tools to further explore those details. You can also do more complex and customized queries with their BioMart interface, and you can perform sequence searches too.

Quick links to tools:

GDR, Genome Database for Rosaceae: http://www.rosaceae.org/

Phytozome: http://www.phytozome.net main site; Peach landing page: http://www.phytozome.net/peach

References:

Verde, I., Abbott, A., Scalabrin, S., Jung, S., Shu, S., Marroni, F., Zhebentyayeva, T., Dettori, M., Grimwood, J., Cattonaro, F., Zuccolo, A., Rossini, L., Jenkins, J., Vendramin, E., Meisel, L., Decroocq, V., Sosinski, B., Prochnik, S., Mitros, T., Policriti, A., Cipriani, G., Dondini, L., Ficklin, S., Goodstein, D., Xuan, P., Fabbro, C., Aramini, V., Copetti, D., Gonzalez, S., Horner, D., Falchi, R., Lucas, S., Mica, E., Maldonado, J., Lazzari, B., Bielenberg, D., Pirona, R., Miculan, M., Barakat, A., Testolin, R., Stella, A., Tartarini, S., Tonutti, P., ArĂºs, P., Orellana, A., Wells, C., Main, D., Vizzotto, G., Silva, H., Salamini, F., Schmutz, J., Morgante, M., & Rokhsar, D. (2013). The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution Nature Genetics DOI: 10.1038/ng.2586

Goodstein, D., Shu, S., Howson, R., Neupane, R., Hayes, R., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., & Rokhsar, D. (2011). Phytozome: a comparative platform for green plant genomics Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr944