Video Tip of the Week: TreeGenes

There was one more Tip of the Week left before our annual review of tips we’ve done, and I wasn’t sure what to cover. And then last week a whole slew of tweets came across my “genome” column referencing some articles in the popular press, best summarized by this tweet that made me laugh:

RT @canuckShuk: O Christmas tree, O Christmas tree, How giant is thy genome! http://t.co/ZgzXgBTU @torontostar

I was very pleased to see that the sequencing of Christmas tree genomes was of broad interest. And it also gave me a chance to cover one of the tools I’ve been meaning to do, but just hadn’t managed to cover yet: TreeGenes.

TreeGenes is a forest tree genome database that’s been around for a while, but as more and more sequencing data will come along from a variety of projects, it will only continue to be important for wrangling the information coming from a number of species. It is a curated database that offers a number of different modules that have key features about the research. You can explore the species for which there is information right now, and the kind of data that they have for it. You can find researchers in this arena with the “colleague” module, and organizations important to this field. There’s a great searchable literature collection.  There are various gene expression data sources, and protein data available too. There is a section called DiversiTree that aims to “provide easy intuitive access to every level of resequencing information, from Tree Sample to SNP” and also has CartograTree, which they describe as “an interactive map utility that allows the visualization and search of genomic, phenotypic, and environmental data. This GIS enabled web application places sequenced or genotyped tree samples in context with available data from Ameriflux, WorldClim, and Try-DB.”

So it’s not just a reference sequence project. There’s a lot of info gathered at TreeGenes that will help you find information on forest trees on a wide range of topics–world wide, in fact.

In my tip I focus on how to access the genome sequence data via their GBrowse installations, but be sure to go over there an check out the full scope of what’s available. It’s a great site.

There was also a really nice study published recently that compared spruce and pine, and I very much wish you could get a Christmas ornament of the Circos diagram in Figure 4. It would be perfect on my tree. (I added the hook, that’s not in the original figure.)

Quick links:

Conifer Genome Network and PineRefSeq:  http://pinegenome.org/ and http://pinegenome.org/pinerefseq/

Swedish spruce genome project site: http://www.congenie.org/

TreeGenes: http://dendrome.ucdavis.edu/treegenes/

Popular press stories: Huge DNA code of the Christmas tree being revealed and A simple Christmas tree, a very complex genome

References:

Wegrzyn, J., Lee, J., Tearse, B., & Neale, D. (2008). TreeGenes: A Forest Tree Genome Database International Journal of Plant Genomics, 2008, 1-7 DOI: 10.1155/2008/412875

Pavy, N., Pelgas, B., Laroche, J., Rigault, P., Isabel, N., & Bousquet, J. (2012). A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers BMC Biology, 10 (1) DOI: 10.1186/1741-7007-10-84