Physcomitrium patens (Phypa_V3)

Physcomitrium patens Assembly and Gene Annotation

About Physcomitrium patens

The mosses (Bryophytes) are non-vascular plants that appeared very early in the fossil record, soon after the transition of plants to terrestrial environments. The Physcomitrium patens genome is therefore valuable in understanding early evolution and adaptation of land plants. Physcomitrium also serves as a model organism for studies of physiology and development. Unlike in higher plants, targeted gene knockouts can be made efficiently in the laboratory, thereby facilitating reverse-genetics approaches to studying gene function. The annotated genome hosted here thereby represents an important resource to the plant research community. Note this species was formerly know as Physcomitrella patens.


The initial draft genome V1 of ecotype Gransden 2004 was published in 2007 and was distributed over ca. 2000 scaffolds. The genome was re-assembled and published in 2018 as V3. The V3 assembly contains 472 Mb in 27 pseudo-chromosomes (1.3% gaps), and 3.9 Mb in 330 unordered nuclear scaffolds. Scaffolds and their associated gene models that were identified as contaminants were removed in three rounds, most recently 2018. The plastid and mitochondrial genome were re-assembled and annotated with the same release, correcting some errors.


Gene annotation v3.3 used large scale RNA-seq data as expression evidence. Annotations predict and map gene models and associated transcripts/proteins using a variety of tools based on cDNA, protein homology and ab initio methods. The release v3.3 contains 32,458 gene models and 86,669 protein-coding transcripts.


  1. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.
    Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R et al. 2018. Plant J. 93:515-533.
  2. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
    Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y et al. 2008. Science. 319:64-69.
  3. Image credit: Pirex at en.wikipedia [Public domain], from Wikimedia Commons.

More information

General information about this species can be found in Wikipedia.



AssemblyPhypa V3, INSDC Assembly GCA_000002425.2, Jan 2018
Database version112.2
Golden Path Length471,852,792
Genebuild byJGI
Genebuild methodImport
Data sourceJoint Genome Institute

Gene counts

Coding genes32,234
Non coding genes440
Small non coding genes438
Long non coding genes2
Gene transcripts87,109