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

More information is available at JGI.

Exploring Populus trichocarpa

Populus trichocarpa in the context of Green Plant evolution

Gene families containing Populus trichocarpa genes can be found by searching at the Viridiplantae, Embryophyte, Tracheophyte, Angiosperm, Rosid Pre- and Post-hexaploidy, Eurosid I and Poplar nodes. Keyword searches (the default) can be performed using either a gene identifier, a gene symbol, ontology id (e.g, GO, PFAM, Panther) or full or partial defline. If you don't have this type of information for your gene of interest, but know something about its functional classification, you can perform an ontology search using a descriptive phrase (e.g., "developmental regulator", "apoptosis inhibition","alkaline phospatase"). This will search the selected ontologies for these phrases, and then use the resulting set of ontology identifiers (e.g, "PF05918", "KOG3913") to search for gene families whose members carry these classifications. Finally, if you don't have keyword or functional information but do have a gene or gene product sequence, you can search for homologous gene families by BLASTing against the (peptide) gene family consensus sequeuences.

The Populus trichocarpa Genome

Use the BROWSE GENOME button at the top of this page to view Populus trichocarpa 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 GENOME button. The browsing environment, Gbrowse, provides overview and detailed views of gene structure. Gbrowse provides a search interface allowing you to look up Populus trichocarpa models by gene name, external identifier, or genomic location. Once you've located a gene model of interest, click on it to go to its detail page. The detail page provides sequence information on the model and its translated peptide. From the detail page you can also jump to viewing the gene in its 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

Bulk data downloads are available from a number of locations:

• BioMart: Choose "Phytozome Genomes" and use the Filter to restrict the data to Populus trichocarpa. You can use other filters to further restrict the data, and then choose which data Attributes to download.
• FTP Site: Phytozome Data. Contains Phytozome-specific data as well as annotation and assembly files for JGI-sourced genomes.

Single Gene Family and Genomic Region data:

• Gene Family page
  • Go to the "Get Data" tab and select either "Get Sequences" or "Get Cluster Data" (which launches BioMart).
  • Go to the "Align Cluster Members" tab and select either "Load Member protein sequences" or "Load Member coding sequences." This will launch Jalview, from which sequences can be downloaded.
• Keyword and BLAST search results page: Data for one or more of the Gene Families found via a keyword search or a BLAST search against a gene family consensus database can be downloaded by selecting "ANALYZE RESULTS/GET DATA" and clicking "Get data for selected families". This will launch BioMart with filters set to retrieve data only for the selected families.
• Gbrowse region page: Use the "Download Alignments", "Download Decorated Fasta", or "Download Sequence" plugins under the "Reports and Analysis" pulldown.