Overview
Physcomitrella patens ssp patens ecotype Gransden 2004 is a species of moss, which is a basal lineage of land plants, having diverged before the acquisition of well developed vasculature. Thus, it stands in an important phylogenetic position for illuminating the evolutionary development of "higher" plants, including those that are model organisms, such as Arabidopsis, and those of commercial importance, such as poplar, corn, soybean, sorghum, and rice. Having the full Physcomitrella genome sequence is a great asset for reconstructing the evolution of plant genomes and for informing the community in the functional genomics of plants, just as the mouse, Fugu, Drosophila, and other genomes have informed animal biology (from JGI - The Joint Genome Institute).
Statistics
This release of Phytozome includes the July 20, 2006 FilteredModels annotation of Physcomitrella patens from JGI - The Joint Genome Institute.
- Genome
- Approximately 480Mb arranged in 27 chromosomes, assembled into 2106 scaffolds.
- Loci
- 39727 loci containing protein-coding transcripts
- Transcripts
- 39796 protein-coding transcripts
Exploring Physcomitrella
- Physcomitrella in the context of Green Plant evolution
- Physcomitrella genes will be found in clusters defined at the Viridiplantae, Embryophyte and Selaginella (crown) nodes. If you know something about the physco 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 the page, enter your search terms, pick the Land Plants node (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 Physcomitrella Genome
- Use the Browse the Genome button at the top of this page to view Physcomitrella 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 Physcomitrella 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 Physcomitrella genes in their evolutionary context. To see this gene's orthologs at the Land Plants 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.
- Downloading Data
- CDS and peptide sequence for individual genes is available from the details page of the Physcomitrella 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.