Planteome Version 1.0 September 2016

Release notes for Planteome 1.0 September 2016

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Number of annotations and bioentities:

Total number of annotations 17,235,484
Total number of unique bioentities (genes, germplasms, QTLs, etc) 1,853,893

 

 

Total number of annotations by taxa:

Species Common name Annotations Total#
Zea mays maize, corn

1,768,298

Brachypodium sylvaticum false brome 1,408,350
Triticum monococcum einkhorn wheat 1,018,251
Arabidopsis thaliana thale cress 738,734
Triticum aestivum common wheat 574,609
Triticum turgidum miracle wheat 443,523
Malus domestica apple 379,173
Physcomitrella patens spreading earthmoss 369,159
Eucalyptus grandis eucalyptus 338,194
Brassica oleracea wild cabbage 322,386
Glycine max soybean 320,196
Populus trichocarpa poplar 310,655
Solanum tuberosum potato 306,333
Oryza sativa rice 303,641
Citrus sinensis sweet orange 302,109
Gossypium raimondii cotton 292,744
Brassica rapa turnip 286,268
Oryza sativa Japonica group japonica rice 281,877
Setaria italica foxtail millet 276,754
Prunus persica peach 268,000
Aegilops tauschii goatgrass 265,436
Picea abies norway spruce 262,270
Triticum urartu red wild einkhorn wheat 256,211
Manihot esculenta cassava 255,177
Oryza sativa Indica group indica rice 252,046
Pinus taeda loblollly pine 246,710
Musa acuminata banana 242,157
Citrus clementina clementine orange 238,705
Arabidopsis lyrata sand cress 233,062
Sorghum bicolor sorghum 232,346
Cicer arietinum chickpea 225,132
Cajanus cajan pigeon pea 222,809
Brachypodium distachyon false brome 218,415
Erythranthe guttata yellow monkey flower 218,310
Capsella rubella pink shepherd's-purse 213,115
Capsicum annuum chili pepper 209,944
Jatropha curcas Barbados nut 207,368
Coffea canephora coffee 204,847
Medicago truncatula barrel medic 202,233
Leersia perrieri cutgrass 201,796
Theobroma cacao cocoa 201,682
Vitis vinifera grape 197,818
Fragaria vesca woodland strawberry 191,200
Nelumbo nucifera lotus 181,440
Ricinis communis castorbean 176,183
Phoenix dactylifera date palm 170,764
Hordeum vulgare barley 162,750
Citrullus lanatus watermelon 151,155
Cucumis sativus cucumber 147,354
Cannabis sativa hemp 139,206
Selaginella moellendorffii spikemoss 124,527
Solanum lycopersicum tomato 113,703
Amborella trichopoda amborella 79,424
Ectocarpus siliculosus brown algae 58,131
Phytophthora infestans potato blight 57,713
Carica papaya papaya 55,633
Lens culinaris subsp. culinaris lentil 32,981
Chlamydomonas reinhardtii green algae 23,085
Triticum monococcum subsp. monococcum einkhorn wheat 13,796
Triticum monococcum subsp. aegilopoides wild einkhorn wheat 13,687
Synechocystis sp. PCC 6803   12,932
Epichloe festucae   9,992
Solanum melongena eggplant 873
Avena sativa common oat 750
Cenchrus americanus pearl millet 568
Gossypium hirsutum upland cotton 472
Zizania palustris northern wildrice 82
Capsicum nightshade 54
Petunia petunia 54
Nicotiana tobacco 41
Zea mays subsp. mays maize, corn 30
Oryza glaberrima african rice 16
Coffea coffee 8
Atropa nightshade 4
Oryza longistaminata red rice 4
Oryza rufipogon brownbeard rice 4
Physalis nightshade 4
Datura Devil's trumpets, moonflowers 3
Solanum chmielewskii wild tomato 3
Solanum pennellii wild tomato 3
Anisodus wild relative of tomato 2
Hyoscyamus henbane 2
Oryza australiensis australian rice 2
Oryza eichingeri   2
Oryza officinalis   2
Picea glauca white spruce 2

 

 

Number of annotations by source database:

Database Annotations Total#
EnsemblPlants 13,436,488
MaizeGDB 1,513,932
Planteome_gene 824,309
TAIR 736,837
cosmoss 224,640
GR_gene 200,884
RAP-DB 73,952
IRIC 54,727
GR_QTL 46,900
GRIN 39,974
GDR 38,600
SGN_germplasm 19,541
Jaiswal_lab 9,561
MaizeGDB_stock 4,914
CRIBI_Vitis 3,410
SOY_QTL 2,396
NASC 1,897
SGN_gene 743
GR_protein 690
Genesys-pgr 389
AgBase 262
GenBank 210
LIS 146
SoyBase 36
SOY_gene 33
Gramene 10
NCBI_gi 3

 

 

 

Total number of annotations by object type:

Object type Annotations Total#
protein 14,982,058
gene_model 1,499,971
mRNA 307,995
gene 222,560
germplasm 121,442
QTL 49,296
gene_product 44,986
tRNA 2,058
RNA 1,333
miRNA 1,080
snoRNA 222
rRNA 58
snRNA 35