Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis

Vitantonio Pantaleo, G. Szittya, Simon Moxon, Laura Miozzi, Vincent Moulton, Tamas Dalmay, J. Burgyán

Research output: Contribution to journalArticle

273 Citations (Scopus)

Abstract

Summary In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at the post-transcriptional level. Many plant miRNAs are conserved, and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have only been found in certain species. Here, we use deep-sequencing, computational and molecular methods to identify, profile, and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues. A total of 24 conserved miRNA families were identified in all four tissues, and 26 known but non-conserved miRNAs were also found. In addition to known miRNAs, we also found 21 new grapevine-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. Furthermore, 21 other plausible miRNA candidates have been described. We have found that many known and new miRNAs showed tissue-specific expression. Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.

Original languageEnglish
Pages (from-to)960-976
Number of pages17
JournalPlant Journal
Volume62
Issue number6
DOIs
Publication statusPublished - Jun 2010

Fingerprint

MicroRNAs
microRNA
Messenger RNA
High-Throughput Nucleotide Sequencing
Vitis
Vitis vinifera
abiotic stress
stress response
RNA
genomics
Gene Expression
gene expression

Keywords

  • High-throughput sequencing
  • MiRNAs
  • RNA silencing
  • Target identification
  • Vitis vinifera

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology
  • Genetics

Cite this

Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. / Pantaleo, Vitantonio; Szittya, G.; Moxon, Simon; Miozzi, Laura; Moulton, Vincent; Dalmay, Tamas; Burgyán, J.

In: Plant Journal, Vol. 62, No. 6, 06.2010, p. 960-976.

Research output: Contribution to journalArticle

Pantaleo, Vitantonio ; Szittya, G. ; Moxon, Simon ; Miozzi, Laura ; Moulton, Vincent ; Dalmay, Tamas ; Burgyán, J. / Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. In: Plant Journal. 2010 ; Vol. 62, No. 6. pp. 960-976.
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