Genome Annotation/V1.6
From PhyscomeProjectWiki
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
- 38,357 mRNA transcript sequences
- 38357 protein sequences
- 18180 5'UTR sequences
- 38357 CDS sequences
- 19,041 3'UTR sequences
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)
