GreeNC

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Arabidopsis thaliana Brassica rapa Chlamydomonas reinhardtii Cucumis sativus Glycine max 155px 155px 155px 155px 155px Genes Transcripts Genes Transcripts Genes Transcripts Genes Transcripts Genes Transcripts Oryzia sativa Prunus persica Solanum lycopersicum Vitis vinifera Zea mays 155px 155px 155px 155px 155px Genes Transcripts Genes Transcripts Genes Transcripts Genes Transcripts Genes Transcripts	Aquí aniria la extenció de "latest news" que hi ha al http://prgdb.crg.eu/
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Long non-coding RNAs (lncRNAs) are non-translated molecules longer than 200 nucleotides that have been extensively studied in mammal genomes. Their roles are diverse, involved in chromatin modifications, transcriptional regulation, and conformational changes in proteins. However, this class of RNAs remains still largely uninvestigated in plants with few exceptions. For instance, IPS1 is a lncRNA expressed upon phosphate starvation and it is believed to counteract the activity of the miR399 on PHO2, which in turn regulates the expression of phosphate transporter genes. In Arabidopsis, the lncRNA COLDAIR was showed to be required to establish and maintain a stable silenced state of FLC by recruiting the histone methylase PRC2, thus affecting flowering time. Finally, in Medicago truncatula, the lncRNA Enod40 was showed to participate in the establishment of symbiotic interactions with soil-bacteria by affecting nodule formation. These findings highlight that lncRNA could be of great interest in plant biology and in breeding as regulating important agronomic traits. In order to deepen our understanding of the role of lncRNAs in plant biology, their comprehensive annotation is mandatory. To achieve this goal, we used a computational approach to annotate lncRNAs from RNA-seq data. Our pipeline let to distinguish lncRNA from protein-coding and other classes of non-coding RNAs, such as rRNA, precursors of miRNAs, etc. We identified thousands of putative lncRNAs using publicly available RNA-seq data in 2 monocotyledons, 7 dicotyledons, and a green algae. The identified sequences will be analyzed in order to assign a putative function and to study their conservation among different taxa. With the aim to facilitate the study of lncRNAs for the plant research community, we present the Green Non-Coding Database (GreeNC) that will provide information about sequence, expression levels, genomic context, ontology and phylogeny of lncRNAs in plants.	Taxon Gene number Transcript number High confidence Hits against transposons miRNA precursors Actinidia chinensis (Ensembl Plants 51) 960 961 591 146 10 Aegilops tauschii (Ensembl Plants 51) 15463 34092 18060 6749 958 Amaranthus hypocondriacus (Phytozome 13) 2075 2083 1476 103 25 Aquilegia coerulea (Phytozome 13) 4321 4868 3545 447 46 Arabidopsis halleri (Ensembl Plants 51) 2448 2508 1814 251 73 Arabidopsis lyrata (Phytozome 13) 2593 2676 1831 280 38 Arabidopsis thaliana (Phytozome 13) 1772 2254 1602 271 14 Arabis alpina (Ensembl Plants 51) 1857 1919 1304 198 22 Beta vulgaris (Phytozome 13) 4843 4980 3538 574 93 Boechera stricta (Phytozome 13) 1932 2019 1416 192 16 Brachypodium stacei (Phytozome 13) 2986 3195 2332 496 104 Brassica napus (Ensembl Plants 51) 9060 9060 6554 526 70 Brassica rapa (Phytozome 13) 2563 2674 1889 209 33 Camelina sativa (Ensembl Plants 51) 6099 6200 4072 477 59 Capsella rubella (Phytozome 13) 1720 1812 1294 127 23 Capsicum annuum (Ensembl Plants 51) 2124 2124 1154 417 6 Chara braunii (Ensembl Plants 51) 595 596 269 171 31 Chenopodium quinoa (Phytozome 13) 1935 1935 1279 214 6 Chondrus crispus (Ensembl Plants 51) 1465 1465 1293 24 31 Chromochloris zofingiensis (Phytozome 13) 1457 1457 1186 113 11 Cicer arietinum (Phytozome 13) 2004 2004 1663 82 7 Cinnamomum kanehirae (Phytozome 13) 1237 1237 806 74 5 Citrullus lanatus (Ensembl Plants 51) 2471 2471 2112 76 22 Coffea canephora (Ensembl Plants 51) 1861 1861 1319 149 16 Corchorus capsularis (Ensembl Plants 51) 2210 2210 1680 80 11 Cucumis melo (Ensembl Plants 51) 5001 5001 3921 414 19 Cucumis sativus (Ensembl Plants 51) 3459 3459 2465 118 22 Cyanidioschyzon merolae (Ensembl Plants 51) 141 141 77 7 1 Cynara cardunculus (Ensembl Plants 51) 1756 1756 1034 115 14 Dioscorea alata (Phytozome 13) 1531 1728 1016 244 15 Eragrostis curvula (Ensembl Plants 51) 6042 6042 4712 509 30 Eragrostis tef (Ensembl Plants 51) 2437 2437 1701 97 14 Glycine max (Phytozome 13) 5137 5978 4246 625 76 Gossypium barbadense (Phytozome 13) 7619 8720 6146 731 72 Gossypium darwinii (Phytozome 13) 8569 9299 6811 639 60 Gossypium hirsutum (Phytozome 13) 8006 9222 6461 787 81 Gossypium mustelinum (Phytozome 13) 7953 9233 6467 793 77 Gossypium raimondii (Ensembl Plants 51) 3800 4555 3000 461 53 Gossypium tomentosum (Phytozome 13) 9009 10090 7504 681 77 Helianthus annuus (Phytozome 13) 8197 8197 5580 795 67 Hordeum vulgare (Phytozome 13) 12659 23867 11477 5740 872 Juglans regia (Ensembl Plants 51) 662 664 404 102 3 Kalanchoe fedtschenkoi (Phytozome 13) 3206 3568 2428 368 66 Lactuca sativa (Phytozome 13) 4949 5395 4095 150 24 Leersia perrieri (Ensembl Plants 51) 3353 3676 2910 297 37 Lupinus albus (Phytozome 13) 4869 4869 3179 881 54 Lupinus angustifolius (Ensembl Plants 51) 1684 1686 1285 102 6 Manihot esculenta (Phytozome 13) 2304 2655 1875 316 55 Marchantia polymorpha (Phytozome 13) 2896 3196 2665 260 47 Medicago truncatula (Ensembl Plants 51) 8986 9093 5288 2584 102 Musa acuminata (Ensembl Plants 51) 2091 2214 1592 127 16 Nicotiana attenuata (Ensembl Plants 51) 3851 3851 2361 924 40 Nymphaea colorata (Phytozome 13) 1763 2055 1356 240 26 Olea europaea (Phytozome 13) 5516 5516 3140 508 21 Oropetium thomaeum (Phytozome 13) 4122 4122 3448 54 13 Oryza barthii (Ensembl Plants 51) 5339 5600 4461 588 51 Oryza brachyantha (Ensembl Plants 51) 4575 4575 3454 422 43 Oryza glaberrima (Ensembl Plants 51) 4807 4807 3334 1017 29 Oryza glumipatula (Ensembl Plants 51) 5402 5837 4536 719 55 Oryza longistaminata (Ensembl Plants 51) 3150 3150 2334 74 16 Oryza meridionalis (Ensembl Plants 51) 4389 4818 3496 832 67 Oryza nivara (Ensembl Plants 51) 6077 6586 4875 757 64 Oryza punctata (Ensembl Plants 51) 3850 4114 3233 440 39 Oryza rufipogon (Ensembl Plants 51) 6357 6801 5006 837 66 Oryza sativa (Phytozome 13) 5395 5724 3788 1435 104 Panicum hallii (Phytozome 13) 2331 2389 2792 522 37 Panicum virgatum (Phytozome 13) 9607 10438 7543 1958 90 Papaver somniferum (Ensembl Plants 51) 5025 5025 3566 432 50 Pistacia vera (Ensembl Plants 51) 1360 1360 952 78 7 Poncirus trifoliata (Phytozome 13) 1660 1795 1233 174 10 Porphyra umbilicalis (Phytozome 13) 934 938 799 20 3 Prunus avium (Ensembl Plants 51) 8673 8673 6035 1530 85 Prunus dulcis (Ensembl Plants 51) 4320 4381 2596 1181 109 Quercus lobata (Ensembl Plants 51) 1873 1873 1011 374 25 Rosa chinensis (Ensembl Plants 51) 11326 11326 6919 2478 104 Saccharum spontaneum (Ensembl Plants 51) 7488 7488 5252 823 51 Salix purpurea (Phytozome 13) 3625 4070 2916 396 48 Sesamum indicum (Ensembl Plants 51) 2515 2515 1783 101 12 Setaria viridis (Phytozome 13) 4897 5427 3948 1025 62 Solanum lycopersicum (Phytozome 13) 4242 4242 2767 471 29 Solanum tuberosum (Phytozome 13) 7181 8005 3302 2022 46 Sorghum bicolor (Phytozome 13) 4454 5107 2973 1726 77 Trifolium pratense (Phytozome 13) 5314 5402 3140 830 44 Triticum aestivum (Ensembl Plants 51) 6619 6710 4833 656 78 Triticum dicoccoides (Ensembl Plants 51) 18737 38102 21006 4356 316 Triticum spelta (Ensembl Plants 51) 8829 8829 6753 559 37 Triticum turgidum (Ensembl Plants 51) 5523 5870 4166 346 18 Triticum urartu (Ensembl Plants 51) 4588 4588 3068 281 16 Vigna angularis (Ensembl Plants 51) 3325 3325 2310 172 31 Vigna radiata (Ensembl Plants 51) 1255 1268 813 80 21 Vigna unguiculata (Phytozome 13) 2719 3083 2270 256 52 Vitis vinifera (Phytozome 13) 2711 2978 2010 243 16 Zea mays (Ensembl Plants 51) 5915 6301 2934 1061 24 Zea mays (Phytozome 13) 4385 7129 4203 252 65