Release Notes 57 (May 2018)

Table of Contents



#Genomes Release Notes

  • New features:
    • Polyploid view for wheat has been enabled, allowing users to view alignments between all 3 wheat components simultaneously.
    • SIFT scores are now displayed on the Genes and regulation view of a gene variant. Here is a sorghum SNP.
  • Updated data:
    • Added gene name synonyms for O. sativa using from database sources such as CGSNL, Oryzabase and Rap-DB.
    • Updated protein features for all (nearly 2 million) plant proteins using InterProScan with version 67 of InterPro.
    • Updated BioMarts for all gene and variation data.
    • 26 new and updated functional genomic databases (see Arabidopsis for example).
    • Tandem repeats annotated by the TRF program are no longer used to soft- and hardmask the genome sequences. This affects sequences retrieved via the API and the files on the FTP site.
  • Updated software



  Species Assembly Gene Annotation
Aegilops tauschii ASM34733v1 GCA_000347335.1
Amborella trichopoda GCA_000471905.1 (AMTR1.0) 2014-01-AGD
Arabidopsis lyrata Araly1.0 Araly1.0
Arabidopsis thaliana TAIR10 AraPort11
Beta vulgaris RefBeet-1.2.2 ENA
Brachypodium distachyon Brachy1.0 Barchy1.2
Brassica napus AST_PRJEB5043_v1 ENA
Brassica oleracea GCA_000092065.1 ENA
Brassica rapa IVFCAASv1 bra_v1.01_SP2010_01
Chlamydomonas reinhardtii v3.0 2007-11-ENA
Chondrus crispus ASM35022v2 ENA

Cucumis sativus (cucumber)

GCA_000004075.2 ENA
Cyanidioschyzon merolae 2008-11-ENA ASM9120v1

Dioscorea rotundata (white Guinea yam)

GCA_002240015.2 ENA
Galdieria sulphuraria ASM34128v1 ENA
Glycine max (soybean) V3 (GCA_000003195.3) 2015-11-ENA

Gossypium raimondii (cotton)

GCA_000327365.1 ENA

Helianthus annuus (common sunflower)

GCA_002127325.1 ENA
Hordeum vulgare (barley) 030312v2 IBSC_1.0
Leersia perrieri GCA_000325765.3 OGE

Lupinus angustifolius (blue lupin)

GCA_001865875.1 ENA

Manihot esculenta (cassava)

GCA_001659605.1 ENA
Medicago truncatula MedtrA17_3.5 2011-11-EnsemblPlants
Musa acuminata (banana) MA1 2012-08-Cirad

Nicotiana attenuata (coyote tobacco)

GCA_001879085.1 ENA
Oryza barthii GCA_000182155.1 OGE Maker (Aug 2013)
Oryza brachyantha GCA_000231095.2 / OGEv1.4b OGEv1.4
Oryza glaberrima GCA_000147395.1 / AGI1.1 (May 2011) 2011-05-AGI (MIPS)
Oryza glumaepatula GCA_000576495.1 OGE Maker (Aug 2013)
Oryza longistaminata v0117-2013Aug OGE
Oryza meridionalis GCA_000338895.1 OGE Maker (Aug 2013)
Oryza nivara GCA_000576065.1 OGE Maker (Aug 2013)
Oryza punctata GCA_000573905.1 OGE Maker (Aug 2013)
Oryza rufipogon PRJEB4137 OGE
Oryza sativa japonica IRGSP-1.0 MSU 7.0
Oryza sativa indica ASM465v1 2010-07-BGI
Ostreococcus lucimarinus v2.0 GCA_000092065.1 JGI
Phaseolus vulgaris (common bean) GCA_000499845.1 ENA
Physcomitrella patens ASM242v1 2011-03-Phypa1.6
Populus trichocarpa JGI 2.0 2010-01-JGI
Prunus persica (peach) Prupe2_0 (GCA_000346465.2) 2017-06-ENA
Selaginella moellendorffii v1.0 2011-05-ENA
Setaria italica (foxtail millet) JGIv2.0 JGIv2.1
Solanum lycopersicum (tomato) SL2.50 ITAG2.3
Solanum tuberosum (potato) 3.0 SolTub_3.0
Sorghum bicolor V3 (GCA_000003195.3) 2017-06-ENA
Theobroma cacao (cocoa) GCA_000403535.1 ENA
Trifolium pratense Trpr TGAC
Triticum aestivum TGACv1 2014-07-PGSBv2.2
Triticum urartu GCA_000347455.1 GCA_000347455.1 (ENA, Apr 2013)
Vitis vinifera IGGP 12x 2012-07-CRIBI
Zea mays (corn) B73_RefGen_v4 MAKER-CSHL


Genetic and Structural Variation

No new and updated genetic/structural variation data since release 54.

Arabidopsis thaliana

Brachypodium sylvaticum

Hordeum vulgare
Oryza glaberrima
Oryza glumaepatula
Oryza sativa Indica
Oryza sativa Japonica
Sorghum bicolor
Solanum lycopersicum
Triticum aestivum
Vitis vinifera
Zea mays


Gene Trees

  • The EnsemblCompara GeneTree database was last updated in release 56. A total of 67,042 GeneTree families were constructed comprising 1,703,219 individual genes (1,892,629 input proteins) from 53 plant genomes (and 5 non-plant outgroups).

Putative Split Genes

  • Split gene predictions were updated in release 56 and are available from Gramene's FTP site.  These are putative gene annotation artifacts (also known as contiguous gene split models) and are based on the latest Ensembl Compara Gene Tree database.  Brief statistics for each species is given below.


Species Count
Arabidopsis lyrata subsp. lyrata 114
Arabidopsis thaliana 29
Beta vulgaris subsp. vulgaris 53
Brachypodium distachyon 115
Brassica oleracea var. oleracea 673
Brassica rapa subsp. pekinensis 106
Cucumis sativus 533
Cyanidioschyzon merolae strain 10D 4
Glycine max 703
Gossypium raimondii 507
Helianthus annuus 739
Hordeum vulgare subsp. vulgare 215
Leersia perrieri 157
Lupinus angustifolius 86
Manihot esculenta 185
Medicago truncatula 282
Musa acuminata subsp. malaccensis 937
Nicotiana attenuata 89
Oryza barthii 223
Oryza brachyantha 216
Oryza glaberrima 398
Oryza glumipatula 222
Oryza meridionalis 152
Oryza nivara 185
Oryza punctata 173
Oryza rufipogon 169
Oryza sativa Indica Group 579
Oryza sativa Japonica Group 602
Ostreococcus lucimarinus CCE9901 12
Phaseolus vulgaris 788
Populus trichocarpa 1185
Prunus persica 90
Setaria italica 239
Solanum lycopersicum 878
Solanum tuberosum 503
Sorghum bicolor 58
Theobroma cacao 62
Trifolium pratense 482
Vitis vinifera 547
Zea mays 244


Genomic alignments and Synteny

Here is a summary of all genomic alignments and syntenies. These correspond to LastZ comparisons between the 8 new genomes and each of Oryza sativa Japonica, Arabidopsis thaliana, and Vitis vinifera. A stats page for each paiwise LastZ alignment is available, see for example the one for P. vulgaris vs V. vinifera and the corresponding synteny map for chromosome 9 of the common bean vs the common grape vine. Also available from Gramene's FTP are Synteny tables.


Protein Annotation, Go, Xref Protein domain information was updated based on the latest InterProScan analysis.



# Pathways

* Pathway Projection Statistics and Status

  • Last updated in release 56b (February 2018). See pathway release 56b notes for a table of pathway projection counts, data source and methods.

* "Cyc" Pathways

  • BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at CyVerse. Summary tables for the Cyc pathway databases created by Gramene is available in release 46 notes.

* Ontologies Release Notes

  • No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.

# Infrastructure

Web Services: Gramene's web services page documents many ways to directly connect to and analyze our databases.

Public MySQL Server

Our partner Ensembl Genomes offers a public, read-only MySQL server with copies of the species-specific and comparative genomic databases that we use. To use this with the mysql command-line client:

$ mysql -P4157 -uanonymous

Please note that the versioning scheme used at this public database differs from ours; Gramene's release 57_92 is set as version 39_92 at Ensembl.