miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection
Micro(mi)RNAs play crucial roles in plant developmental processes and in defense responses to biotic and abiotic stresses. 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 orde...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-07-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.01034/full |
| _version_ | 1811328300585320448 |
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| author | Walter Chitarra Walter Chitarra Chiara Pagliarani Simona Abbà Paolo Boccacci Giancarlo Birello Marika Rossi Sabrina Palmano Cristina Marzachì Irene Perrone Giorgio Gambino |
| author_facet | Walter Chitarra Walter Chitarra Chiara Pagliarani Simona Abbà Paolo Boccacci Giancarlo Birello Marika Rossi Sabrina Palmano Cristina Marzachì Irene Perrone Giorgio Gambino |
| author_sort | Walter Chitarra |
| collection | DOAJ |
| description | Micro(mi)RNAs play crucial roles in plant developmental processes and in defense responses to biotic and abiotic stresses. 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 reorganize the high quantity of available data, we produced “miRVIT,” the first database of all novel grapevine miRNA candidates characterized 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. Conserved and novel miRNAs cataloged in miRVIT were then used for analyzing Vitis vinifera plants infected by Flavescence dorée (FD), one of the most severe phytoplasma diseases affecting grapevine. The analysis of small RNAs from healthy, recovered (plants showing spontaneous and stable remission of symptoms), and FD-infected “Barbera” grapevines showed that FD altered the expression profiles of several miRNAs, including those involved in cell development and photosynthesis, jasmonate signaling, and disease resistance response. The application of miRVIT in a biological context confirmed the effectiveness of the followed approach, especially for the identification of novel miRNA candidates in grapevine. miRVIT database is available at http://mirvit.ipsp.cnr.it.Highlights: The application of the newly produced database of grapevine novel miRNAs to the analysis of plants infected by Flavescence dorée reveals key roles of miRNAs in photosynthesis and jasmonate signaling. |
| first_indexed | 2024-04-13T15:22:49Z |
| format | Article |
| id | doaj.art-f09f74b790af4cc1b557ce670e2e434d |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T15:22:49Z |
| publishDate | 2018-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-f09f74b790af4cc1b557ce670e2e434d2022-12-22T02:41:37ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-07-01910.3389/fpls.2018.01034389134miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée InfectionWalter Chitarra0Walter Chitarra1Chiara Pagliarani2Simona Abbà3Paolo Boccacci4Giancarlo Birello5Marika Rossi6Sabrina Palmano7Cristina Marzachì8Irene Perrone9Giorgio Gambino10Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyViticultural and Enology Research Centre, Council for Agricultural Research and Economics, Conegliano, ItalyInstitute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyInstitute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyInstitute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyResearch Institute on Sustainable Economic Growth, National Research Council of Italy, Turin, ItalyInstitute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyInstitute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyInstitute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyInstitute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyInstitute for Sustainable Plant Protection, National Research Council of Italy, Turin, ItalyMicro(mi)RNAs play crucial roles in plant developmental processes and in defense responses to biotic and abiotic stresses. 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 reorganize the high quantity of available data, we produced “miRVIT,” the first database of all novel grapevine miRNA candidates characterized 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. Conserved and novel miRNAs cataloged in miRVIT were then used for analyzing Vitis vinifera plants infected by Flavescence dorée (FD), one of the most severe phytoplasma diseases affecting grapevine. The analysis of small RNAs from healthy, recovered (plants showing spontaneous and stable remission of symptoms), and FD-infected “Barbera” grapevines showed that FD altered the expression profiles of several miRNAs, including those involved in cell development and photosynthesis, jasmonate signaling, and disease resistance response. The application of miRVIT in a biological context confirmed the effectiveness of the followed approach, especially for the identification of novel miRNA candidates in grapevine. miRVIT database is available at http://mirvit.ipsp.cnr.it.Highlights: The application of the newly produced database of grapevine novel miRNAs to the analysis of plants infected by Flavescence dorée reveals key roles of miRNAs in photosynthesis and jasmonate signaling.https://www.frontiersin.org/article/10.3389/fpls.2018.01034/fulldisease resistancejasmonatemiRNAsphytoplasmatarget genesunivocal database |
| spellingShingle | Walter Chitarra Walter Chitarra Chiara Pagliarani Simona Abbà Paolo Boccacci Giancarlo Birello Marika Rossi Sabrina Palmano Cristina Marzachì Irene Perrone Giorgio Gambino miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection Frontiers in Plant Science disease resistance jasmonate miRNAs phytoplasma target genes univocal database |
| title | miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection |
| title_full | miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection |
| title_fullStr | miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection |
| title_full_unstemmed | miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection |
| title_short | miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection |
| title_sort | mirvit a novel mirna database and its application to uncover vitis responses to flavescence doree infection |
| topic | disease resistance jasmonate miRNAs phytoplasma target genes univocal database |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.01034/full |
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