Release notes for Planteome 1.0 September 2016
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