Planta

, Volume 247, Issue 5, pp 1191–1202 | Cite as

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

Original Article
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Abstract

Main conclusion

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 

Abbreviations

CircRNAs

Circular RNAs

GO

Gene Ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

Notes

Acknowledgements

This research was supported financially by the National Natural Science Foundation of China (Grant nos. 31772252, 31471863, 31372046, 31521092, and 31672110). Hubei Provincial Natural Science Foundation for Innovative Group (2017CFA018) and the International Foundation for Science No. C/5148-2.

Supplementary material

425_2018_2857_MOESM1_ESM.jpg (3.6 mb)
Suppl. Fig. S1 Sanger sequencing further confirmed head-to-tail back-splicing of 11 selected circRNAs (JPEG 3657 kb)
425_2018_2857_MOESM2_ESM.xlsx (19 kb)
Suppl. Table S1 Primers used in this study (XLSX 19 kb)
425_2018_2857_MOESM3_ESM.xlsx (65 kb)
Suppl. Table S2 Genome-wide identification of circRNAs in two genotypes of the trifoliate orange (XLSX 65 kb)
425_2018_2857_MOESM4_ESM.xlsx (4.4 mb)
Suppl. Table S3 The 558 circRNA sequences from two genotypes of the trifoliate orange (XLSX 4459 kb)
425_2018_2857_MOESM5_ESM.xlsx (30 kb)
Suppl. Table S4 Alternative circularization of trifoliate orange circRNAs (XLSX 29 kb)
425_2018_2857_MOESM6_ESM.xlsx (36 kb)
Suppl. Table S5 Differential expression of circRNAs between precocious trifoliate orange and its wild type (XLSX 36 kb)
425_2018_2857_MOESM7_ESM.xlsx (23 kb)
Suppl. Table S6 The different biological metabolism pathways from up-regulated circRNA host genes were identified by KEGG pathway analysis (XLSX 23 kb)
425_2018_2857_MOESM8_ESM.xlsx (23 kb)
Suppl. Table S7 The different biological metabolism pathways from down-regulated circRNA host genes were identified by KEGG pathway analysis (XLSX 22 kb)
425_2018_2857_MOESM9_ESM.xlsx (20 kb)
Suppl. Table S8 Differential expression of circRNAs predicted as putative miRNA targets (XLSX 19 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhanChina
  2. 2.College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhanChina

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