Genome Annotation/V1.6

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The Physcomitrella patens V1.6 genome annotation.

Contents

Release Notes

Improved Locus Definition (cosmoss.org gene ids; CGIs)

With V1.6 we improved the locus definition and thus had to alter cosmoss gene ids.

Example CGI
Pp1sX_YVx.n 
Pp1s1_2V2.1 as in Physcomitrella patens assembly V1 scaffold_1 locus 2 annotation V1.2  splice variant 1 

I.e. the CGIs from the previous V1.2/V1.5 release do not necessarily represent the same loci. If you want to compare versions we offer a mapping table (link comes soon) that addresses this issue.

We use the CGIs as primary accession numbers on cosmoss.org.

Phypa_ids

Phypa- or protein-ids are provided as first entry in the Alias field. If the annotation was not changed as compared to V1.2 the Phypa_id was retained (1579 mRNAs;) otherwise it was assigned a new Phypa_id. E.g:

ID=Pp1s3_40V6.1 Alias=Phypa_64577,PHYPADRAFT_64577 ...
ID=Pp1s1_2V6.1	Alias=Phypa_422229 ...
new Phypa_ids assigned by cosmoss.org begin at
Phypa_300000

Splice Variants

mRNAs derived from the same locus, i.e. splice variants are children of the same gene feature (indicated by the number after the V6):

gene    ID=Pp1s1_5V6;Name=Pp1s1_5V6
mRNA    ID=Pp1s1_5V6.1;Parent=Pp1s1_5V6;Alias=Phypa_422107
mRNA    ID=Pp1s1_5V6.2;Parent=Pp1s1_5V6;Alias=Phypa_422004

Downloads genome annotation version 1.6

Please cite the following paper if you use the V1.6 genome annotation for your work:

Zimmer, A.D., D. Lang, K. Buchta, S. Rombauts, T. Nishiyama, M. Hasebe, Y. van de Peer, S.A. Rensing, R. Reski (2013): Reannotation and extended community resources of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics 14, 498.

In addition, if you use any of the released files please provide this site and the release as a reference:

current: V1.6 2012.3 https://www.cosmoss.org/physcome_project/wiki/Downloads

Gene structure annotation

GFF3

V1.6 protein coding GFF3
32,275 gene structures of 38,357 protein coding transcripts in GFF3 format.
V1.6 non-protein coding GFF3
non-protein coding genes/regions (798 rRNA, 432 tRNA, 229 miRNA, 213 snRNA, 6 SRP) in GFF3 format.

FASTA

Functional annotation - genonaut dumps

The community-curated genonaut annotation (descriptions, gene names, protein names, GO) is dumped regularly and available as release and master branch in a bitbucket repository. The master branch will soon be configured to reflect nightly dumps.

Latest Release 2012.3

cosmoss.genonaut.gene_name.txt
gene name tab-delimited table (including annotator information)
cosmoss.genonaut.protein_name.txt
protein name tab-delimited table (including annotator information)
cosmoss.genonaut.aliases.txt
gene aliases tab-delimited table (including annotator information)
cosmoss.genonaut.description.txt
description lines tab-delimited table (including annotator information)
cosmoss.genonaut.annot
Transcript/Protein-wise GO annotation in BLAST2GO annotation format
cosmoss.genonaut.gaf2
Transcript/Protein-wise GO annotation in GO Annotation File Format 2.0 (GAF2.0)
cosmoss.genonaut.map
Locus-wise GO annotation in topGO input format
cosmoss.genonaut.txt
Full text annotation genonaut database including author information

Master branch - Nightly-build

If you use these include Nightly-built downloaded on XX-XX-XXXX in your methods section.

cosmoss.genonaut.gene_name.txt
gene name tab-delimited table (including annotator information)
cosmoss.genonaut.protein_name.txt
protein name tab-delimited table (including annotator information)
cosmoss.genonaut.aliases.txt
gene aliases tab-delimited table (including annotator information)
cosmoss.genonaut.description.txt
description lines tab-delimited table (including annotator information)
cosmoss.genonaut.descriptions.txt
description lines tab-delimited table
cosmoss.genonaut.annot
Transcript/Protein-wise GO annotation BLAST2GO annotation format
cosmoss.genonaut.gaf2
Transcript/Protein-wise GO annotation in GO Annotation File Format 2.0 (GAF2.0)
cosmoss.genonaut.map
Locus-wise GO annotation in topGO input format
cosmoss.genonaut.txt
Full text annotation genonaut database including author information

Additional functional annotations

cosmoss.TAPScan.csv
TAPScan Transcription factor classification Lang et al. 2010 Genome Biology and Evolution 2, 488-503
cosmoss.mapman.txt
MapMan annotation D. Lang (unpublished)

Mapping to old annotation releases

Conversion of P. patens gene accessions numbers (Excel xls file)
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