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Overview

StatusReference proteome
Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome%5Fredundancy">more...</a>)</p> 47,782
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000006727
Taxonomy3218 - Physcomitrium patens
Straincv. Gransden 2004
Genome assemblyi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000002425.2 from EnsemblPlants full
Genome annotationi EnsemblPlants
Buscoi <p>The Benchmarking Universal Single-Copy Ortholog (BUSCO) assessment tool is used, for eukaryotic and bacterial proteomes, to provide quantitative measures of UniProt proteome data completeness in terms of expected gene content. BUSCO scores include percentages of complete (C) single-copy (S) genes, complete (C) duplicated (D) genes, fragmented (F) and missing (M) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment, and the name of the taxonomic lineage dataset used.</p> C:88.8%[S:0.6%,D:88.2%],F:1.4%,M:9.9%,n:1614 embryophyta_odb10
Completenessi <p>Complete Proteome Detector (CPD) is an algorithm which employs statistical evaluation of the completeness and quality of proteomes in UniProt, by looking at the sizes of taxonomically close proteomes. Possible values are 'Standard', 'Close to Standard' and 'Outlier'.</p> Unknown

The moss Physcomitrella patens is a model organism for studying the evolution of land plants. As a Bryophyte this organism sits midway along the evolutionary path between unicellular aquatic algae and flowering land plants.

Physcomitrella patens has a very efficient mechanism of homologous recombination which can be used to create targeted genetic modifications. It also shows alternation of generations, with the haploid phase of the life-cycle being dominant. These characteristics make it an excellent experimental material. It is used to examine the key genetic changes involved in adaptation to water stress and temperature variation, associated with life on land, and the loss of flagellae, associated with aquatic life.

The reference proteome for Physcomitrella patens is derived from the genome published in 2008 (www.ncbi.nlm.nih.gov/pubmed/18079367 ). The genome has a haploid chromosome number of 27 containing nearly 500 Mb, with 35,000 protein-coding genes. Further details of the genome assembly are available at the 'Physcomitrella patens resource' (www.cosmoss.org).

Componentsi <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationProteins
Unplaced
19
Chromosome 12993
Chromosome 22748
Chromosome 32671
Chromosome 42242
Chromosome 51945
Chromosome 62095
Chromosome 71989
Chromosome 81698
Chromosome 91833
Chromosome 101885
Chromosome 111973
Chromosome 121736
Chromosome 131545
Chromosome 141979
Chromosome 151831
Chromosome 161862
Chromosome 171769
Chromosome 181372
Chromosome 191435
Chromosome 201651
Chromosome 211455
Chromosome 221429
Chromosome 231452
Chromosome 241379
Chromosome 251020
Chromosome 261036
Chromosome 27615
Mitochondrion42
Chloroplast85
Unassembled WGS sequence0

Publications

  1. "The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants."
    Terasawa K., Odahara M., Kabeya Y., Kikugawa T., Sekine Y., Fujiwara M., Sato N.
    Mol. Biol. Evol. 24:699-709(2007) [PubMed] [Europe PMC] [Abstract]
  2. "Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus."
    Sugiura C., Kobayashi Y., Setsuyuki A., Sugita C., Sugita M.
    Nucleic Acids Res. 31:5324-5331(2003) [PubMed] [Europe PMC] [Abstract]
  3. "The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution."
    Lang D., Ullrich K.K., Murat F., Fuchs J., Jenkins J., Haas F.B., Piednoel M., Gundlach H., Van Bel M., Meyberg R., Vives C., Morata J., Symeonidi A., Hiss M., Muchero W., Kamisugi Y., Saleh O., Blanc G.
    Rensing S.A.
    Plant J. 93:515-533(2018) [PubMed] [Europe PMC] [Abstract]
  4. "The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants."
    Rensing S.A., Lang D., Zimmer A.D., Terry A., Salamov A., Shapiro H., Nishiyama T., Perroud P.-F., Lindquist E.A., Kamisugi Y., Tanahashi T., Sakakibara K., Fujita T., Oishi K., Shin-I T., Kuroki Y., Toyoda A., Suzuki Y.
    Boore J.L.
    Science 319:64-69(2008) [PubMed] [Europe PMC] [Abstract]
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