[Gramene-announce] Announcing Gramene release #60: New & updated genomes, pathways and other features
Jaiswal, Pankaj - OSU
jaiswalp at science.oregonstate.edu
Wed Feb 13 15:24:13 EST 2019
Hello Everyone,
The Gramene project team is pleased to announce its Release #60 with the
Genome section <http://ensembl.gramene.org/genome_browser/index.html>
providing access to information on 2,162,056 genes and 58 reference
plant genomes. It includes new reference genome of /Arabidopsis halleri/
and updates to several existing genomes. 1,891,391 protein-coding genes
are organized in 93,194 gene families. The Plant Reactome
<http://plantreactome.gramene.org>, Gramene's pathway portal hosts
pathway projections for 79 species ranging from unicellular autotrophs
to higher plants. In this release, we have extended orthology-based
pathway projections for 1 new species: /Arabidopsis halleri
<http://plants.ensembl.org/Arabidopsis_halleri>//, and /revised pathways
for /several species,
<http://plants.ensembl.org/Solanum_lycopersicum/Info/Index>/based on
their recent genome updates; added 10 new curated pathways for reference
species /Oryza sativa/ (total curated reference pathways are 293).
Gramene is a curated, open-source, integrated data resource for
comparative functional genomics in crops and model plant species. The
genome databases were built in direct collaboration with Ensembl Plants
and the Plant Reactome database was produced in collaboration with the
Reactome project.
*GENOMES*
* *New genomes: *
o /Arabidopsis halleri
<http://ensembl.gramene.org/Arabidopsis_halleri/Info/Index>/:
assembly GCA_900078215
<https://www.ebi.ac.uk/ena/data/view/GCA_900078215>, annotation
doi:10.5061/dryad.gn4hh.
<https://datadryad.org/resource/doi:10.5061/dryad.gn4hh?show=full>
* *Updated genomes:*
o /Aegilops tauschii
<http://ensembl.gramene.org/Aegilops_tauschii/Info/Index>/:
updated assembly and annotation to version Aet v4.0
(GCA_002575655 <https://www.ebi.ac.uk/ena/data/view/GCA_002575655>).
o /Solanum lycopersicum
<http://ensembl.gramene.org/Solanum_lycopersicum>/: updated
assembly (GCA_000188115.3
<https://www.ebi.ac.uk/ena/data/view/GCA_000188115.3>) and
annotation (ITAG3.0, except unplaced genes).
o /Glycine max <http://ensembl.gramene.org/Glycine_max>:/ updated
assembly (GCA_000004515.4
<https://www.ebi.ac.uk/ena/data/view/GCA_000004515.4>) and
annotation (Rel. 137, Version 4, Glycine_max_v2.1).
o /Vigna radiata <http://ensembl.gramene.org/Vigna_radiata>/:
updated annotation (vigra.VC1973A.gnm6.ann1.M1Qs).
o /Physcomitrella patens/
<http://ensembl.gramene.org/Vigna_radiata>: updated annotation
(V3.3
<https://genomevolution.org/coge/ExperimentView.pl?eid=11065>).
* *New & Updated data:
*
o /Triticum aestivum
<http://ensembl.gramene.org/Triticum_aestivum/Info/Index>/:
Inter-Homeologous Variants (IHVs) were added.
o /Lupinus angustifolius
<http://ensembl.gramene.org/Lupinus_angustifolius>/: genes from
previous release were added.
o /Arabidopsis thaliana:
<http://ensembl.gramene.org/Arabidopsis_thaliana>/ TAIR10 is now
the unique source of ncRNA annotations.
o /Nicotiana attenuata
<http://ensembl.gramene.org/Nicotiana_attenuata>/: mapped
microarray probes were updated.
o /Zea mays: <http://ensembl.gramene.org/Zea_mays>/ mapped
microarray probes were updated.
o BioMarts <http://ensembl.gramene.org/biomart/martview/> for all
gene and variation data.
o Updated split gene predictions
<ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/split_genes/>
from peptide comparative genomics
<http://ensemblgenomes.org/info/data/peptide_compara>.
* *Updated software:* *Updated genome browser, database schema, and
API to Ensembl 95 software
<http://www.ensembl.info/2019/01/09/ensembl-95-is-out/>.*
*PATHWAYS* (Plant Reactome <http://plantreactome.gramene.org>):
For details see: Plant Reactome Release Summary
<http://plantreactomedev.oicr.on.ca/index.php?option=com_content&view=article&id=66&Itemid=360&lang=en>
- Version 17 (Gramene r60): Here is the summary of updates made to plant
pathways.
* *Website and coding updates* : The latest Plant Reactome pathway
data has been re-indexed and made available via Gramene search.
* *Curation of reference rice pathways:***We have added 10 newly
curated pathways and 3 "container" pathways, and updated 2 existing
pathways, resulting in a total of 293 reference rice pathways.
*
*New Pathways*:
* Regulation of embryo development
* Maternal tissue PCD
* Cell cycle regulation
* Aleurone layer formation
* Regulatory network of nutrient accumulation
* Regulation of seed size
* Regulation of leaf development
* HSFA7/ HSFA6B-regulatory network-induced by drought and ABA.
* SNAC1 transcription network involved in drought and salinity
tolerance
* Arsenic uptake and detoxification
* Regulatory Network of Nutrient Accumulation
*
*Updated/renamed pathways:*
* Flower development
* Thiosulfate disproportionation III (rhodanese)
* *Pathway Projections:***We have extended orthology-based pathway
projections for 1 new species: /Arabidopsis halleri/
<http://plants.ensembl.org/Arabidopsis_halleri>. Plant Reactome now
hosts pathway projections for 79 species ranging from unicellular
autotrophs to higher plants. In addition, we have revised pathways
for /several species/
<http://plants.ensembl.org/Solanum_lycopersicum/Info/Index>based on
their recent genome updates (see genome section).
The Plant Reactome increasingly includes curated regulatory and
developmental pathways, which require more reference DNA and RNA
sequence elements, in addition to the traditional protein-coding
elements. These sequence elements are not included in
Reactome orthoinference at this time, although we are actively working
to enhance the projection process to include these elements on projected
pathways in future releases.
Please let us know if you have questions or suggestions.
The Gramene Team
www.gramene.org.
--
Pankaj Jaiswal, PhD
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA
Ph.: +1-541-737-8471
Fax: +1-541-737-3573
email: jaiswalp at oregonstate.edu
Web: http://jaiswallab.cgrb.oregonstate.edu
http://icbo-conference.org
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