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

More information is available at JGI (note that the JGI info refers to release v1.1).

Exploring Physcomitrella patens

Physcomitrella patens in the context of Green Plant evolution

Gene families containing Physcomitrella patens genes can be found by searching at the Viridiplantae, Embryophyte and Physcomitrella 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 Physcomitrella patens Genome

Use the BROWSE GENOME button at the top of this page to view Physcomitrella patens 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 Physcomitrella patens 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 Physcomitrella patens. 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.