[Gramene-announce] Announcing Gramene Knowledgebase release #61 (April 2019)
Jaiswal, Pankaj - OSU
jaiswalp at science.oregonstate.edu
Fri May 3 16:59:00 EDT 2019
The Gramene Knowledgebase Team is pleased to announce its *Release #61
<http://www.gramene.org/release-notes-61>* with the Genome section
<http://ensembl.gramene.org/genome_browser/index.html> providing access
to information on 2,264,698 genes and 61 reference plant genomes. It
includes three new reference genomes: kiwifruit (/Actinidia chinensis)
<http://ensembl.gramene.org/Actinidia_chinensis>/, and two ecotypes of
Hall's panicgrass (/Panicum hallii/ FIL2
<http://ensembl.gramene.org/Panicum_hallii_fil2>) and (/Panicum
hallii/ HAL2) <http://ensembl.gramene.org/Panicum_hallii_hal2>,
and updates to several existing genomes. This release also includes 109
manually curated maize gene models
<http://news.gramene.org/curated_maize_v4_gene_models> as a GFF file
<ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/gff3/zea_mays/curated_apollo_annotations_maize_v4.gff3>
to attach as a custom track in Gramene's genome browser (and will soon
be also available as a permanent track). The Plant Reactome
<http://plantreactome.gramene.org>, Gramene's pathway portal hosts
pathway projections for 82 species including those in the Genome section
ranging from unicellular autotrophs to higher plants. Total curated
reference pathways are 298. See more details on the release #61 page.
Gramene Knowledgebase 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. Core funding for the project is
provided by the National Science Foundation, USA.
------------------------------------------------------------------------
* *New Plant Genomes: *
1. Kiwifruit (/Actinidia chinensis/
<http://ensembl.gramene.org/Actinidia_chinensis>): assembly and
annotation GCA_003024255.1
<https://www.ebi.ac.uk/ena/data/view/GCA_003024255.1>
2. /Panicum hallii/ FIL2
<http://ensembl.gramene.org/Panicum_hallii_fil2>: PHallii_v3.1
assembly and annotation GCA_002211085.2
<https://www.ebi.ac.uk/ena/data/view/GCA_002211085.2>
3. /Panicum hallii/ HAL2
<http://ensembl.gramene.org/Panicum_hallii_hal2>: PhalliiHAL_v2.1
assembly and annotation GCA_003061485.1
<https://www.ebi.ac.uk/ena/data/view/GCA_003061485.1>
* *Updated genomes:*
1. /Oryza sativa Japonica/ <http://ensembl.gramene.org/oryza_sativa>:
updated nonOrganelle gene annotation from RAP-DB
<https://rapdb.dna.affrc.go.jp> version 2018-11-26 and added
stable_id mappings to previous annotation.
2. /Solanum lycopersicum/
<http://ensembl.gramene.org/Solanum_lycopersicum> (tomato): added
ITAG3.0 unplaced gene models (Chr0)
* *New & Updated data: *
1. /Triticum aestivum
<http://ensembl.gramene.org/Triticum_aestivum/Info/Index>/ (bread
wheat): added 31,779 markers from the 35K Axiom SNP array (provided
byCerealsDB <http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB>).
2. /Triticum dicoccoides/
<http://ensembl.gramene.org/Triticum_dicoccoides>(Emma Zavitan
wheat): added polyploid view.
3. /Vigna radiata/ <http://ensembl.gramene.org/Vigna_radiata>: added
stable_id mappings to previous annotation.
4. /Physcomitrella patens
<http://ensembl.gramene.org/Physcomitrella_patens>/: added stable_id
mappings to previous annotation.
5. New manually curated maize gene models
<http://news.gramene.org/curated_maize_v4_gene_models> (custom
genome track may be set up using this GFF file
<ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/gff3/zea_mays/curated_apollo_annotations_maize_v4.gff3>).
6. New whole-genome alignments for /A. chinensis/
<http://ensembl.gramene.org/Actinidia_chinensis>, /P. hallii/ FIL2
<http://ensembl.gramene.org/Panicum_hallii_fil2> and /P. hallii/
HAL2 <http://ensembl.gramene.org/Panicum_hallii_hal2>, see WGA
section <http://news.gramene.org/node/496/edit?render=overlay#WGA>.
7. New synteny data for /A. chinensis/
<http://ensembl.gramene.org/Actinidia_chinensis>, /P. hallii/ FIL2
<http://ensembl.gramene.org/Panicum_hallii_fil2>, /P. hallii/ HAL2
<http://ensembl.gramene.org/Panicum_hallii_hal2> and /Sorghum
bicolor <http://ensembl.gramene.org/Sorghum_bicolor/Info/Index>/,
see Synteny section
<http://news.gramene.org/node/496/edit?render=overlay#Synteny>.
8. BioMarts <http://ensembl.gramene.org/biomart/martview> for all gene
and variation data.
9. Updated split gene predictions
<ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/splitgenes/> from
peptide comparative genomics
<http://ensemblgenomes.org/info/data/peptide_compara>.
* *Updated software:*Updated genome browser, database schema, and API
to *Ensembl 96 software
<http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/>.*
* *Genetic and Structural Variation : *31,779 markers from the 35K
Axiom SNP array were added to the /Triticum aestivum
<http://ensembl.gramene.org/Triticum_aestivum/Info/Index>/ (Wheat)
genome. They were provided by CerealsDB
<http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB> and designed
by Affymetrix.
* *Compara gene trees: *The Ensembl Compara GeneTree database updated.
A total of 92,708 GeneTree families were constructed comprising
1,948,793 individual protein coding genes from 61 plant genomes with
2,158,277 input proteins.
* *Identifying Split genes*: Updated split genes for the current
release are available on FTP site
<ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/splitgenes/>.
These are putative gene annotation artifacts (also known as
contiguous gene split models) and are based on the latest Ensembl
Compara Gene Tree database.
* *Whole genome alignments and Synteny*: Kiwifruit and two Panicum
genomes were included in the whole genomic alignments
<http://ensembl.gramene.org/compara_analyses.html> and synteny data
sets.
------------------------------------------------------------------------
* *Plant Pathways*
o *Wesbite updates: *For user and data security, SSL (Secure
Sockets Layer) has now been implemented on Plant Reactome. The
entire site and all services are now available over https. The
latest Plant Reactome pathway data has also been re-indexed and
made available via Gramene search.
o *Curation of reference rice pathways:***
+ We have added 4 newly curated pathways, 2 updated pathways
and 1 "container" pathway, resulting in a total of 298
reference rice pathways.
+ *New Pathways:*
1. Root hair development
2. Phytic Acid biosynthesis (lipid independent)
3. Response to aluminum stress
4. Root-specific gene-network of NAC10_TF induced by
drought, salinity, and ABA
+ *Updated pathways*:
1. HSFA7-regulatory network induced by drought and ABA
2. SNAC1 transcription network involved in drought and
salinity tolerance
+ *Pathway Projection Statistics:***We have extended
orthology-based pathway projections for three new species:
/Actinidia chinensis/
<http://plants.ensembl.org/Actinidia_chinensis> (kiwi
fruit), /Panicum hallii FIL2
<http://plants.ensembl.org/Panicum_hallii_fil2>/ ("Hall's
panicgrass"), and /Panicum hallii var. hallii HAL2
<http://plants.ensembl.org/Panicum_hallii_hal2>/. Plant
Reactome now hosts pathway projections for 82 species
ranging from unicellular autotrophs to higher plants.
Please let us know if you have questions or suggestions.
The Gramene Team
www.gramene.org <http://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
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