Search Physcomitrella patens

Description

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 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.

Genome Sequencing and Gene Prediction (release JGI Ppatens v1.6)

Information from JGI

The haploid genome of Physcomitrella patens ssp patens ecotype Gransden 2004 is estimated to be approximately 480 Mb contained in 27 pairs of chromosomes, and was sequenced to approximately 8.1 X depth.

The genome assembly remained unchanged since release v.1.1 in 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 approximately 480 Mb. Half of the assembly is contained in 111 scaffolds, all at least 1.3 Mb in length. The length-weighted mean contig size is 72.5 kb.
Gene annotations are now updated to v1.6 from Cosmoss - The Physcomitrella patens resource. Annotations were 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 32272 gene models and 38354 protein-coding transcripts. Scaffold and their associated gene models that were identified as contaminants in 2009 have been removed.

Gramene/Ensembl Genomes Annotation

Additional annotations generated by the Gramene/Ensembl Genomes projects include:

The standard set of Gramene analyses detailed here.
Phylogenetic gene trees and whole-genome alignments with several plant and metazoan species, using Ensembl's Compara pipeline.

References

Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13. PubMed ID: 18079367

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