Physcomitrella patens subsp patens v1.1
For information on the most current version of this organism's data, click here: the Phytozome Physcomitrella site.

Project Status

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 release v.1.1 was annotated using the JGI annotation pipeline. Gene models and associated transcripts/proteins are predicted or mapped using a variety of tools based on cDNA, protein homology and ab initio methods. The current release contains approximately 35,938 gene models supported by known Physcomitrella genes and available Physcomitrella EST and cDNA data.

Approximately 95% of Physcomitrella full-length cDNAs mapped to the v.1.1 assembly. Average gene length is 2.4 kb and average transcript length is 1.2 kb, with the average protein containing 363 amino acids. There are approximately 4.87 exons per gene averaging 245 bp each with intron spacing of 310 bp. Gene functions have been automatically assigned based on homology to known genes. Manual curation of these annotations will start shortly.

Assembly 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, have a total length of approximately 480 Mb composed of 19,136 contigs. 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.

Collaborators

Links

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.

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.