GreeNC

A database of plants lncRNAs

Arabidopsis thaliana

Brassica rapa

Chlamydomonas reinhardtii

Cucumis sativus

Glycine max

Oryza sativa

Prunus persica

Solanum lycopersicum

Vitis vinifera

Zea mays

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.

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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.

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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.

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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.

News

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Statistics

Taxon	Gene number	Transcript number	High confidence	Hits against transposons	miRNA precursors
Amborella_trichopoda	5698	5698	4156	103	347
Ananas_comosus	3376	3376	1674	163	935
Arabidopsis_lyrata	4363	4363	2622	158	60
Arabidopsis_thaliana	2752	3008	1720	1018	63
Brachypodium_distachyon	4828	5584	3648	870	1024
Capsella_grandiflora	1338	1394	1013	90	27
Capsella_rubella	1395	1458	1069	100	20
Carica_papaya	3986	3987	2439	980	181
Chlamydomonas_reinhardtii	583	619	135	217	450
Citrus_clementina	2056	2192	1553	149	34
Citrus_sinensis	2344	2562	1788	171	42
Coccomyxa_subellipsoidea_C-169	668	668	469	33	92
Cucumis_sativus	1817	1929	1390	152	32
Eucalyptus_grandis	4499	4639	3629	204	103
Eutrema_salsugineum	1588	1669	1238	85	25
Fragaria_vesca	3503	3503	2412	728	133
Glycine_max	5974	6689	4749	832	133
Gossypium_raimondii	3520	4216	3037	256	55
Linum_usitatissimum	2598	2598	1955	37	46
Malus_domestica	4126	4126	2565	688	83
Manihot_esculenta	3137	3468	2660	266	90
Medicago_truncatula	9373	9676	5793	2567	286
Micromonas_pusilla_CCMP1545	651	651	230	19	300
Micromonas_pusilla_RCC299	351	351	199	6	48
Mimulus_guttatus	2169	2333	1591	186	59
Musa_acuminata	4071	4071	2525	170	90
Oryza_sativa_Japonica_Group	4995	5237	3601	1148	119
Ostreococcus_lucimarinus	501	501	209	9	128
Phaseolus_vulgaris	1838	1946	1450	152	30
Physcomitrella_patens	6888	9690	8390	907	299
Populus_trichocarpa	4997	5569	4111	434	124
Prunus_persica	2803	3301	2216	526	85
Ricinus_communis	4198	4198	3127	174	215
Selaginella_moellendorffii	906	906	409	28	26
Setaria_italica	3240	3492	2159	507	669
Solanum_lycopersicum	3440	3440	2448	423	60
Solanum_tuberosum	5974	6680	2976	2682	184
Sorghum_bicolor	4624	5305	2682	1737	1057
Spirodela_polyrhiza	2111	2111	1536	86	174
Theobroma_cacao	4137	4268	3306	461	59
Triticum_aestivum	23359	38820	21132	5714	1039
Vitis_vinifera	2526	2526	1624	296	23
Volvox_carteri	1097	1134	592	222	371
Zea_mays	16857	18110	10229	4004	2192
Zostera_marina	1393	1393	1014	55	23