Identification of Known and Novel <i>Arundo donax</i> L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis
MicroRNAs (miRNAs) are a class of non-coding molecules involved in the regulation of a variety of biological processes. They have been identified and characterized in several plant species, but only limited data are available for <i>Arundo donax</i> L., one of the most promising bioenerg...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-04-01
|
| Series: | Life |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-1729/12/5/651 |
| _version_ | 1797498466728935424 |
|---|---|
| author | Silvia Rotunno Claudia Cocozza Vitantonio Pantaleo Paola Leonetti Loris Bertoldi Giorgio Valle Gian Paolo Accotto Francesco Loreto Gabriella Stefania Scippa Laura Miozzi |
| author_facet | Silvia Rotunno Claudia Cocozza Vitantonio Pantaleo Paola Leonetti Loris Bertoldi Giorgio Valle Gian Paolo Accotto Francesco Loreto Gabriella Stefania Scippa Laura Miozzi |
| author_sort | Silvia Rotunno |
| collection | DOAJ |
| description | MicroRNAs (miRNAs) are a class of non-coding molecules involved in the regulation of a variety of biological processes. They have been identified and characterized in several plant species, but only limited data are available for <i>Arundo donax</i> L., one of the most promising bioenergy crops. Here we identified, for the first time, <i>A. donax</i> conserved and novel miRNAs together with their targets, through a combined analysis of high-throughput sequencing of small RNAs, transcriptome and degradome data. A total of 134 conserved miRNAs, belonging to 45 families, and 27 novel miRNA candidates were identified, along with the corresponding primary and precursor miRNA sequences. A total of 96 targets, 69 for known miRNAs and 27 for novel miRNA candidates, were also identified by degradome analysis and selected slice sites were validated by 5′-RACE. The identified set of conserved and novel candidate miRNAs, together with their targets, extends our knowledge about miRNAs in monocots and pave the way to further investigations on miRNAs-mediated regulatory processes in <i>A. donax</i>, Poaceae and other bioenergy crops. |
| first_indexed | 2024-03-10T03:33:47Z |
| format | Article |
| id | doaj.art-67f2d3d14fe34dd1a87fc9c4c564ccd4 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T03:33:47Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-67f2d3d14fe34dd1a87fc9c4c564ccd42023-11-23T11:49:23ZengMDPI AGLife2075-17292022-04-0112565110.3390/life12050651Identification of Known and Novel <i>Arundo donax</i> L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome AnalysisSilvia Rotunno0Claudia Cocozza1Vitantonio Pantaleo2Paola Leonetti3Loris Bertoldi4Giorgio Valle5Gian Paolo Accotto6Francesco Loreto7Gabriella Stefania Scippa8Laura Miozzi9Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, ItalyDepartment of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Via San Bonaventura 13, 50145 Florence, ItalyNational Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Research Unit of Bari, CNR, 70126 Bari, ItalyNational Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Research Unit of Bari, CNR, 70126 Bari, ItalyBMR Genomics S.R.L, Via Redipuglia 22, 35131 Padova, ItalyBMR Genomics S.R.L, Via Redipuglia 22, 35131 Padova, ItalyNational Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce 73, 10135 Torino, ItalyNational Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce 73, 10135 Torino, ItalyDepartment of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, ItalyNational Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce 73, 10135 Torino, ItalyMicroRNAs (miRNAs) are a class of non-coding molecules involved in the regulation of a variety of biological processes. They have been identified and characterized in several plant species, but only limited data are available for <i>Arundo donax</i> L., one of the most promising bioenergy crops. Here we identified, for the first time, <i>A. donax</i> conserved and novel miRNAs together with their targets, through a combined analysis of high-throughput sequencing of small RNAs, transcriptome and degradome data. A total of 134 conserved miRNAs, belonging to 45 families, and 27 novel miRNA candidates were identified, along with the corresponding primary and precursor miRNA sequences. A total of 96 targets, 69 for known miRNAs and 27 for novel miRNA candidates, were also identified by degradome analysis and selected slice sites were validated by 5′-RACE. The identified set of conserved and novel candidate miRNAs, together with their targets, extends our knowledge about miRNAs in monocots and pave the way to further investigations on miRNAs-mediated regulatory processes in <i>A. donax</i>, Poaceae and other bioenergy crops.https://www.mdpi.com/2075-1729/12/5/651giant reedmiRNAssmall RNAsdegradome |
| spellingShingle | Silvia Rotunno Claudia Cocozza Vitantonio Pantaleo Paola Leonetti Loris Bertoldi Giorgio Valle Gian Paolo Accotto Francesco Loreto Gabriella Stefania Scippa Laura Miozzi Identification of Known and Novel <i>Arundo donax</i> L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis Life giant reed miRNAs small RNAs degradome |
| title | Identification of Known and Novel <i>Arundo donax</i> L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis |
| title_full | Identification of Known and Novel <i>Arundo donax</i> L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis |
| title_fullStr | Identification of Known and Novel <i>Arundo donax</i> L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis |
| title_full_unstemmed | Identification of Known and Novel <i>Arundo donax</i> L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis |
| title_short | Identification of Known and Novel <i>Arundo donax</i> L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis |
| title_sort | identification of known and novel i arundo donax i l micrornas and their targets using high throughput sequencing and degradome analysis |
| topic | giant reed miRNAs small RNAs degradome |
| url | https://www.mdpi.com/2075-1729/12/5/651 |
| work_keys_str_mv | AT silviarotunno identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT claudiacocozza identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT vitantoniopantaleo identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT paolaleonetti identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT lorisbertoldi identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT giorgiovalle identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT gianpaoloaccotto identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT francescoloreto identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT gabriellastefaniascippa identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis AT lauramiozzi identificationofknownandnoveliarundodonaxilmicrornasandtheirtargetsusinghighthroughputsequencinganddegradomeanalysis |