The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic

PLoS Genet. 2021 Mar 19;17(3):e1009461. doi: 10.1371/journal.pgen.1009461. eCollection 2021 Mar.

Abstract

Long noncoding RNAs (lncRNAs) are emerging as important regulators in plant development, but few of them have been functionally characterized in fruit ripening. Here, we have identified 25,613 lncRNAs from strawberry ripening fruits based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries, most of which exhibited distinct temporal expression patterns. A novel lncRNA, FRILAIR harbours the miR397 binding site that is highly conserved in diverse strawberry species. FRILAIR overexpression promoted fruit maturation in the Falandi strawberry, which was consistent with the finding from knocking down miR397, which can guide the mRNA cleavage of both FRILAIR and LAC11a (encoding a putative laccase-11-like protein). Moreover, LAC11a mRNA levels were increased in both FRILAIR overexpressing and miR397 knockdown fruits, and accelerated fruit maturation was also found in LAC11a overexpressing fruits. Overall, our study demonstrates that FRILAIR can act as a noncanonical target mimic of miR397 to modulate the expression of LAC11a in the strawberry fruit ripening process.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Fragaria / genetics*
  • Fragaria / growth & development*
  • Fruit / genetics*
  • Gene Editing
  • Gene Expression Regulation, Plant*
  • Genetic Association Studies
  • MicroRNAs / genetics
  • Models, Biological
  • Phenotype
  • RNA, Guide, CRISPR-Cas Systems
  • RNA, Long Noncoding*
  • RNA, Messenger / genetics
  • RNA, Plant*

Substances

  • MicroRNAs
  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA, Plant

Grants and funding

This research received funding from National Natural Science Foundation of China Grant number: 31960138 and 31401077 to DW, National Natural Science Foundation of China Grant number 31800224 to RH, Natural Science Foundation of Jiangxi Province Grant number 20171ACB20001 to DW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.