Overview
With a genome of just over 500 million letters of genetic code, Populus trichocarpa was sequenced eight times over to attain the highest quality standards. Poplar was chosen as the first tree DNA sequence decoded because of its relatively compact genetic complement, some 50 times smaller than the genome of pine, making the poplar an ideal model system for trees.
The poplar genome, divided into 19 chromosomes, is four times larger than the genome of the first plant sequenced four years ago, Arabidopsis thaliana. Analysis of the assembled genome reveals a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Poplar genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages (from JGI - The Joint Genome Insitute and Tuskan, et.al.).
Statistics
This release of Phytozome includes the JGI v1.1 release of the Populus trichocarpa genome.
- Genome
- Approximately 500Mb arranged in 19 chromosomes, assembled into 22136 scaffolds
- Loci
- 54299 loci containing protein-coding transcripts
- Transcripts
- 54374 protein-coding transcripts
Exploring Poplar
- Populus trichocarpa in the context of Green Plant evolution
- Poplar genes will be found in clusters defined at the Viridiplantae, Embryophyte, Tracheophyte, Angiosperm, and Rosid nodes. If you know something about the poplar gene you're interested in (e.g., its JGI model name, a descriptive phrase), you can select "search" from the menu at the top of this page, enter your search terms, pick one of the above nodes (or All nodes), and search. The gene clusters you find can then be examined in detail, with summary pages that include descriptive and functional (domain) annotation, syntenic context, and links to each cluster's ancestors and descendants. If you don't have keyword information but do have a gene or gene product sequence, you can search for related gene clusters using BLAST (click on "search" and then select the BLAST tab).
- The Poplar Genome
- Use the Browse the Genome button at the top of this page to view Poplar gene models in their full genomic context. Alternatively, if you'd like to search the genome for regions homologous to a particular sequence, use the BLAST against the genome button. The browsing environment, Gbrowse, provides overview and detailed views of gene structure. Gbrowse provides a search interface allowing you to look up Poplar models by JGI model name or location. Once you've located a gene model of interest, click on it to go to its detail page (e.g, here). The detail page provides sequence information on the model and its translated peptide. From the detail page you can also jump to viewing Poplar genes in their evolutionary context. To see this gene's orthologs at the Angiosperm node, click on the Cluster link on the detail page. If you'd like to see what other ancestral gene's share sequence similarity with this gene, click on the detail page's Phytozome BLAST link, which will pull up similar gene clusters at whichever Phytozome node you choose.
- Downloading Data
- CDS and peptide sequence for individual genes is available from the details page of the Poplar Gbrowse environment. To get there from a Cluster Summary page, however, you'll need to click the "Display Options" tab and make sure that "Reference ID" column is selected. Then expand all the "Genes in the Cluster" rows (by clicking on the
icon near the Org heading) and click on the "[PAC]" link, which will take you to the detail page for that model. You can also get gene sequences for all the members of one or more clusters from any Cluster Summary, Phytozome BLAST results, or Search Results page, by launching Jalview (by clicking links for Multiple Sequence Alignments"), which will provide access to CDS sequence or peptide sequence of the members of the gene clusters you selected. If you're are interested in bulk downloads of all data (gene models, proteomes, genomic sequence), this is available directly from JGI.