Physcomitrella patens Assembly and Gene Annotation

About Physcomitrella 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 Physcomitrella patens genome is therefore valuable in understanding early evolution and adaptation of land plants. Physcomitrella 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.

Assembly

Information from JGI: The haploid genome of Physcomitrella patens ssp. patens ecotype Gransden 2004 is estimated to be ~480 Mbp contained in 27 pairs of chromosomes, and was sequenced to approximately 8.1x depth.

The genome assembly has remained unchanged since release v.1.1 (March 2007). Approximately 5.5 million shotgun reads were initially assembled using JAZZ. There are a total of 2,106 scaffolds, composed of 19,136 contigs, with a total length of ~480 Mbp. Half of the assembly is contained in 111 scaffolds, all at least 1.3 Mbp in length. The length-weighted mean contig size is 72.5 kbp.

Annotation

Gene annotations are now updated to v1.6 from Cosmoss - The Physcomitrella patens resource. Annotations were originally made by JGI using a pipeline to predict and map gene models and associated transcripts/proteins using a variety of tools based on cDNA, protein homology and ab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 v1.6 contains 32,272 gene models and 38,354 protein-coding transcripts. Scaffold and their associated gene models that were identified as contaminants in 2009 have been removed.

Links

References

  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.

Statistics

Summary

AssemblyPhypa V3, INSDC Assembly GCA_000002425.2, Jan 2018
Database version94.2
Base Pairs471,852,792
Golden Path Length471,852,792
Genebuild by26
Genebuild methodImported from ENA
Data sourceJoint Genome Institute

Gene counts

Coding genes31,248
Non coding genes440
Small non coding genes438
Long non coding genes2
Pseudogenes3
Gene transcripts31,691

About this species