Micro(mi)RNAs play crucial roles in plant developmental processes, as well as in defence responses to biotic and abiotic stresses, through post-transcriptional control of several biological pathway intermediates. In the last years, many works on small RNAs in grapevine (Vitis spp.) were published, and several conserved and putative novel grapevine-specific miRNAs were identified. In order to reorganise the high quantity of available data, we produced 'miRVIT', the first database of all novel grapevine miRNA candidates characterised so far, and still not deposited in miRBase. To this aim, each miRNA accession was renamed, repositioned in the last version of the grapevine genome and compared with all the novel and conserved miRNAs detected in grapevine. Overall, 901 sequences referred to as novel miRNAs were found of which 621 are 20-22 nt long and classified as 469 unique novel miRNAs. However, miRNA* sequences were identified for only 150 accessions, and 45 of these were found in at least two different works. Only 5% (45 of 901) of the novel miRNAs previously identified in grapevine could be considered robust unique novel miRNAs. Conserved and novel miRNAs catalogued in miRVIT were then used for analyzing V. vinifera plants infected by Flavescence dorée (FD). FD is considered one of the most severe phytoplasma diseases affecting grapevine, and the spontaneous, complete and stable remission of symptoms (recovery) is a still poorly understood phenomenon. The analysis of small RNAs from healthy (H), recovered (R) and FD-infected (FD) cv. Barbera grapevines revealed key roles of miRNAs in cell development and photosynthesis (vvi-miR156, vvi-miR166, vvi_miC137-3p), jasmonate signalling (vvi-miR319, vvi-miR167) and disease resistance response (vvi-miR482, vvi_miC1031-5p, vvi_miC64-5p), associated to regulation of FD-infection and recovery processes. The application of miRVIT in a biological context confirmed the effectiveness of the approach, especially for the identification of novel miRNA candidates in grapevine.
A novel grapevine microRNAs database and its application to investigate Vitis vinifera responses to Flavescence dorée infection
Chitarra W;Pagliarani C;Abbà S;Boccacci P;Rossi M;Palmano S;Perrone I;Gambino G
2018
Abstract
Micro(mi)RNAs play crucial roles in plant developmental processes, as well as in defence responses to biotic and abiotic stresses, through post-transcriptional control of several biological pathway intermediates. In the last years, many works on small RNAs in grapevine (Vitis spp.) were published, and several conserved and putative novel grapevine-specific miRNAs were identified. In order to reorganise the high quantity of available data, we produced 'miRVIT', the first database of all novel grapevine miRNA candidates characterised so far, and still not deposited in miRBase. To this aim, each miRNA accession was renamed, repositioned in the last version of the grapevine genome and compared with all the novel and conserved miRNAs detected in grapevine. Overall, 901 sequences referred to as novel miRNAs were found of which 621 are 20-22 nt long and classified as 469 unique novel miRNAs. However, miRNA* sequences were identified for only 150 accessions, and 45 of these were found in at least two different works. Only 5% (45 of 901) of the novel miRNAs previously identified in grapevine could be considered robust unique novel miRNAs. Conserved and novel miRNAs catalogued in miRVIT were then used for analyzing V. vinifera plants infected by Flavescence dorée (FD). FD is considered one of the most severe phytoplasma diseases affecting grapevine, and the spontaneous, complete and stable remission of symptoms (recovery) is a still poorly understood phenomenon. The analysis of small RNAs from healthy (H), recovered (R) and FD-infected (FD) cv. Barbera grapevines revealed key roles of miRNAs in cell development and photosynthesis (vvi-miR156, vvi-miR166, vvi_miC137-3p), jasmonate signalling (vvi-miR319, vvi-miR167) and disease resistance response (vvi-miR482, vvi_miC1031-5p, vvi_miC64-5p), associated to regulation of FD-infection and recovery processes. The application of miRVIT in a biological context confirmed the effectiveness of the approach, especially for the identification of novel miRNA candidates in grapevine.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
