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

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.

Characterization and Cloning of Grape Circular RNAs Identified the Cold Resistance-Related Vv-circATS1

“…Such functions include promoting the transcription of host genes via binding with RNA polymerase II in the nucleus (Li et al, 2015), decreasing the expression of linear RNA (Tan et al, 2017), and promoting ES (Conn et al, 2017). Thus, the cognate linear genes of circRNAs are always used for KEGG and GO functional enrichment analyses to determine the potential function of circRNAs (Wang et al, 2017b;Zhou et al, 2017;Pan et al, 2018;Zeng et al, 2018). In this study, cold response represented differentially enriched GO terms under cold stress, implying that circRNA host genes participate in the cold response (Supplemental Fig.…”

Transcriptome-Wide Identification and Characterization of Circular RNAs in Leaves of Chinese Cabbage (Brassica rapa L. ssp. pekinensis) in Response to Calcium Deficiency-Induced Tip-burn

“…With the three samples at 0, 3 and 6 d after Ca 2+ deficiency treatment, we could identify changes in the circRNAs expression at different stages and trace the underlying responding circRNAs to calcium deficiency-induced tip-burn in Chinese cabbage. Analysis the host genes of circRNAs is one of the primary methods to provide valuable hints regarding the functions of circRNAs, considering that the function of only a few circRNAs has been clarified 42 . Therefore, we conducted GO and KEGG analysis on host genes of the different expressed circRNAs in this study.…”

Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato Leaves

“…Recently, plant circRNAs have been identified and reported in Arabidopsis (Ye et al, 2015), barley (Darbani et al, 2016), rice (Ye et al, 2015), tomato (Zuo et al, 2016), soybean (Zhao W. et al, 2017), wheat (Wang et al, 2017b), cotton , kiwi (Wang Z.P. et al, 2017), potato (Zhou et al, 2018b), maize (Chen et al, 2018), and orange (Zeng et al, 2018). The identification of circRNAs accelerates the understanding of the functions of circRNAs in different biological processes in plants.…”