The Joint Genome Institute is pleased to announce public release of v1.1 annotation of the Physcomitrella patens ssp patens genome, which can be accessed through the JGI Genome Portal.

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

ASPB Past President and past Editor-in-Chief of The Plant Cell Ralph Quatrano and colleagues led the moss genome research effort. Knowledge gained from the moss genome, with its early development in evolution, is expected to be helpful to the study of many plants. Quatrano is professor at Washington University, St. Louis.

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.

The genome assembly release v.1.1 was annotated using the JGI annotation pipeline. Gene models and associated transcripts/proteins were predicted or mapped using a variety of tools based on cDNA, protein homology and ab initio methods. The current release (FilteredModels3) contains 35,938 gene models supported by known Physcomitrella patens ssp patens genes and available Physcomitrella patens ssp patens EST and cDNA data. The gene models have the following average properties:

Gene length 2.4 kb
Transcript length 1.2 kb
Protein length 363 aa
Exon frequency 4.87 exons per gene
Exon length 245 nt
Intron length 310 nt
Gene density 74.87 genes/Mbp scaffold

The genes were predicted by the following methods:

Total models 35,938
Known genes 210 (1%)
Homology-based 13,150 (37%)
ab initio 22,578 (63%)

The genes were validated by:

ESTs 8,998 (25%)
Swissprot hit 13,340 (37%)
Pfam hit 13,613 (38%)
manually curated 1,676 (5%)

Contact: Ralph Quatrano