Transcriptome-wide identification and functional prediction of novel and flowering-related circular RNAs from trifoliate orange (Poncirus trifoliata L. Raf.)

Planta. 2018 May;247(5):1191-1202. doi: 10.1007/s00425-018-2857-2. Epub 2018 Feb 7.

Abstract

A total of 558 potential circular RNAs (circRNAs) were identified in citrus, and these were analyzed and compared. One hundred seventy-six differentially expressed circRNAs were identified in two genotypes of trifoliate orange. Circular RNAs (circRNAs) play diverse roles in transcriptional control and microRNA (miRNA) function. However, little information is known about circRNAs in citrus. To identify citrus circRNAs and investigate their functional roles, high-throughput sequencing of precocious trifoliate orange (an early-flowering trifoliate orange mutant, Poncirus trifoliata L. Raf.) and its wild type was performed. A total of 558 potential circRNAs were identified by bioinformatic analysis, and 86.02% of these were sense-overlapping circRNAs. Their sequence features, alternative circularization, and other characteristics were investigated in this study. Compared with the wild type, 176 circRNAs were identified as differentially expressed circRNAs, 61 were significantly up-regulated and 115 were down-regulated in precocious trifoliate orange, indicating that they may play an important role in the early flowering process. Alternative circularization and differential expression of some circRNAs were verified by Sanger sequencing and real-time polymerase chain reaction. The functions of differentially expressed circRNAs and their host genes were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. We found that many differentially expressed circRNAs had abundant miRNA binding sites: 29 circRNAs were found to act as the 16 miRNA targets. Overall, these results will help to reveal the biological functions of circRNAs in growth and development of citrus.

Keywords: Alternative circularization; Back-splicing sites; Citrus; Host genes; microRNAs.

MeSH terms

  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Gene Library
  • Genotype
  • Poncirus / genetics*
  • Poncirus / growth & development
  • RNA / genetics*
  • RNA / physiology
  • RNA, Circular
  • RNA, Plant / genetics*
  • RNA, Plant / physiology
  • Real-Time Polymerase Chain Reaction

Substances

  • RNA, Circular
  • RNA, Plant
  • RNA