Release Notes 56 (January 2018)


See also notes for release 56b (focus on new pathways).


Table of Contents

#Genomes Release Notes



  Species Assembly Gene Annotation

Cucumis sativus (cucumber)

GCA_000004075.2 ENA

Dioscorea rotundata (white Guinea yam)

GCA_002240015.2 ENA

Gossypium raimondii (cotton)

GCA_000327365.1 ENA

Helianthus annuus (common sunflower)

GCA_002127325.1 ENA

Lupinus angustifolius (blue lupin)

GCA_001865875.1 ENA

Manihot esculenta (cassava)

GCA_001659605.1 ENA

Nicotiana attenuata (coyote tobacco)

GCA_001879085.1 ENA
Phaseolus vulgaris (common bean) GCA_000499845.1 ENA


  Species Assembly Gene Annotation
Updated Glycine max (soybean) V3 (GCA_000003195.3) 2015-11-ENA
Oryza sativa japonica IRGSP-1.0 MSU 7.0
Prunus persica (peach) Prupe2_0 (GCA_000346465.2) 2017-06-ENA
Sorghum bicolor V3 (GCA_000003195.3) 2017-06-ENA


  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
Cyanidioschyzon merolae 2008-11-ENA ASM9120v1
Galdieria sulphuraria ASM34128v1 ENA
Hordeum vulgare (barley) 030312v2 IBSC_1.0
Leersia perrieri GCA_000325765.3 OGE
Medicago truncatula MedtrA17_3.5 2011-11-EnsemblPlants
Musa acuminata (banana) MA1 2012-08-Cirad
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 indica ASM465v1 2010-07-BGI
Ostreococcus lucimarinus v2.0 GCA_000092065.1 JGI
Physcomitrella patens ASM242v1 2011-03-Phypa1.6
Populus trichocarpa JGI 2.0 2010-01-JGI
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
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 updated to include updated barley, sorghum, corn and wheat. 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 this release 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

The current Gramene release includes 24 new synteny pairs (see 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

In build 55, Plant Reactome released several new data files, available for download. Visit the Download section of the Plant Reactome web site to learn more.

* Pathway Projection Statistics and Status

  • Last updated in release 52 (November 2016). See pathway release 52 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 56_91 is set as version 38_91 at Ensembl.