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Physcomitrella patens genome view
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  BLAST search Physcomitrella patens sequences
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At present, none of the contigs from the current public WGS assembly have been placed on chromosomes so you cannot browse the sequence data by chromosome. You can find sequenced regions of interest by:

  • querying Map Viewer for a known gene name, symbol, or locus-tag, e.g., ppabcb23 or PHYPADRAFT_48230
  • querying Map Viewer for accession numbers, e.g., XM_001786438 or NW_001866428.
  • searching Entrez Gene for Physcomitrella patens genes that have been annotated on the genome.
  • searching by sequence using BLAST against the genome. Results from a BLAST sequence alignment can be displayed in Map Viewer by clicking on the Genome View button or on the accession numbers of the results.

     Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Bryophytina; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella; Physcomitrella patens
Joint Genome Institute (JGI) has sequenced the genome of Physcomitrella patens to about 8.6x coverage. Sequencing was done using whole genome shotgun (WGS) strategy and the genome was assembled using the JAZZ genome assembly system. None of the contigs have been placed on chromosomes in this first version of the WGS assembly.

The P. patens genome is approximately 480 Mb organized as 27 pairs of chromosomes. The genome assembly consists of 2106 scaffolds, 1443 of which are annotated. The sequence contains 35,938 predicted and annotated gene models. Details regarding sequencing, annotation, and analysis of the genome can be found at Rensing et al. Science 319(5859):245-50, 2007.

The NCBI Map Viewer provides graphical displays of features on the Physcomitrella patens genome sequence assembly. Some of the map features that can be seen along the sequence include NCBI contigs (the Contig map), the WGS sequences (the Component map), and the location of aligned transcripts from P. patens (rnaPpa) and Arabidopsis thaliana (rnaAt). The genes on sequence map include both known genes and putative genes based on JGI submission. The complete set of Gnomon predicted gene models can be viewed on the ab initio map.

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