Abstract
Soybean oil is composed of fatty acids and glycerol. The content and composition of fatty acids partly determine the quality of soybean seeds. Circular RNAs (circRNAs) are endogenous non-coding RNAs that competitively bind to microRNAs (miRNAs) through miRNA recognition elements, thereby acting as sponges to regulate the expression of target genes. Although circRNAs have been identified previously in soybean, only their expression has been investigated without exploration of the competitive endogenous RNAs (ceRNAs) network of circRNAs-miRNAs-mRNAs. In this study, circRNAs in immature pods of a low linolenic acid soybean Mutant 72’ (MT72) and the wild-type control ‘Jinong 18’ (JN18) were systematically identified and analyzed at 30 and 40 days after flowering using high-throughput sequencing technology. We identified 6377 circRNAs, of which 114 were differentially expressed. Gene ontology and KEGG pathway analyses of targeted mRNAs in the ceRNAs network indicated that the differentially expressed circRNAs may be involved in fatty acid transport, suggesting that circRNAs may play a post-transcriptional regulatory role in soybean oil synthesis. This study provides a foundation for future exploration of the function of circRNAs in soybean and presents novel insights to guide further studies of plant circRNAs.
This is a preview of subscription content, log in via an institution to check access.
Source statistics of the circRNAs. c Number of circRNAs-host genes that generated different count of circRNAs in soybean. d The number of circRNAs and back-spliced reads in four samples. e The length distribution of circRNAs. f The circle plot shows the distribution of the identified circRNAs in soybean chromosomes and their expression levels. The outermost layer represents all soybean chromosomes (Chr01–Chr20). The inner layer of the figure represents the samples, which are respectively JN_40, JN_30, MT_40, and MT_30 from the outside to the inside, with 3 samples in each group. The denser lines indicate more circRNAs distribution. g The circle plot shows the distribution of the identified different types of circRNAs in soybean chromosomes and their expression levels. The circle layer represents the type of circRNAs, and from outside to inside, it is circRNAs generated by introns, exons, and intergenic
Similar content being viewed by others
Data Availability
Not applicable.
Code availability
Not applicable.
References
Chen X, Sun S, Liu F et al (2019) A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum). BMC Genomics 20:856–869. https://doi.org/10.1186/s12864-019-6236-6
Conn VM, Hugouvieux V, Nayak A et al (2017) A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants 3:17053. https://doi.org/10.1038/nplants.2017.53
Darbani B, Noeparvar S, Borg S (2016) Identification of Circular RNAs from the parental genes involved in multiple aspects of cellular metabolism in barley. Front Plant Sci 7:776. https://doi.org/10.3389/fpls.2016.00776
Gao Y, Wang J, Zhao F (2015) CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Bio 16:4. https://doi.org/10.1186/s13059-014-0571-3
Gao Z, Li J, Luo M et al (2019) Characterization and cloning of grape circular RNAs identified the cold resistance-related Vv-circATS1. Plant Physiol 180:966–985. https://doi.org/10.1104/pp.18.01331
He XY, Guo SR, Wang Y (2020) Systematic identifification and analysis of heat-stress-responsive lncRNAs, circRNAs and miRNAs with associated co-expression and ceRNA networks in cucumber (Cucumis sativus L.). Physiol Plant 168:736–754. https://doi.org/10.1111/ppl.12997
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360. https://doi.org/10.1038/nmeth.3317
Kim D, Salzberg SL (2011) TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 12:R72. https://doi.org/10.1186/gb-2011-12-8-r72
Lu TT, Cui LL, Zhou Y, et al (2015) Transcriptome-wide investigation of circular RNAs in rice. RNA 21:2076–2087. http://www.rnajournal.org/cgi/doi/10.1261/rna.052282.115
Langmead B, Salzberg L (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923
Lei BJ, Yin GC, Lu CH, et al (1988) Soybean seed development and the process of fat and protein accumulation. Chinese Journal of Oil Crops 4:10–13. http://www.cnki.com.cn/Article/CJFD1988-ZGYW198804002.htm (in Chinese)
Li CL, Qin SW, Bao LH et al (2020) Identifification and functional prediction of circRNAs in Populus Euphratica Oliv. heteromorphic leaves. Genomics 112:92–98. https://doi.org/10.1016/j.ygeno.2019.01.013
Li JL, Cui J, Dai CH et al (2021) Whole-transcriptome RNA sequencing reveals the global molecular responses and CeRNA regulatory network of mRNAs, lncRNAs, miRNAs and circRNAs in response to salt stress in sugar beet (Beta vulgaris). Int J Mol Sci 22:289. https://doi.org/10.3390/ijms22010289
Li WB, Feng L, Song W, et al (2017) Accumulation dynamics of fatty acid in soybean seed and screening of candidate gene related to linolenic acid metabolism. Journal of Northeast Agricultural University. 48:1–8. http://en.cnki.com.cn/Article_en/CJFDTotal-DBDN201711001.htm (in Chinese)
Lin F, Xian LD, Hao Z et al (2018) Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing. BMC Genomics 1:663. https://doi.org/10.1186/s12864-018-5054-6
Liu HM, Yu WW, Wu JT et al (2020) Identification and characterization of circular RNAs during wood formation of poplars in acclimation to low nitrogen availability. Planta 251:47. https://doi.org/10.1007/s00425-020-03338-w
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J 17:10–2. https://doi.org/10.14806/ej.17.1.200
Ma SY, Liang Q, Yin TF, et al (1999). Fatty acid composition analysis during soybean seed development. Soybean Science 2:125 -129. http://www.cnki.com.cn/Article/CJFDTotal-DDKX902.005.htm (in Chinese)
Meng XW, Zhang PJ, Chen Q et al (2018) Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development. BMC Genomics 19:607. https://doi.org/10.1186/s12864-018-4993-2
Privett OS, Dougherty KA, Erdahl WL et al (1973) Studies on the lipid composition of developing soybeans. J Am Oil Chem Soc 50:516–520. https://doi.org/10.1007/BF02640523
Piwecka M, Glažar P, Hernandez-Miranda LR, et al (2017) Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science 357:6357. https://science.sciencemag.org/content/357/6357/eaam8526
Pan T, Sun X, Liu Y et al (2017) Heat stress alters genome-wide profiles of circular RNAs in Arabidopsis. Plant Mol Biol 96:217–229. https://doi.org/10.1007/s11103-017-0684-7
Robinson MD, Mccarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. https://doi.org/10.1093/bioinformatics/btp616
Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK (1976) Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad 73:3852–3856. https://doi.org/10.1073/pnas.73.11.3852
Saltzman J, Gawad C, Wang PL et al (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7:e3073. https://doi.org/10.1371/journal.pone.0030733
Shannon P, Markiel A, Ozier O, et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504. http://www.genome.org/cgi/doi/10.1101/gr.1239303
Shen JF, Ge JF, Zheng SY et al (2021) Integrative analysis of differential circular RNA and long non-coding RNA profiles and associated competing endogenous RNA networks in esophageal squamous cell carcinoma. Funct Integr Genomics 21:125–138. https://doi.org/10.1007/s10142-020-00765-6
Tan JJ, Zhou ZJ, Niu YJ, Sun XY (2017) Identification and functional characterization of tomato circRNAs derived from genes involved in fruit pigment accumulation. Sci Rep 7:8594. https://doi.org/10.1038/s41598-017-08806-0
Tian Y, Xu Y, Wang HW et al (2019) Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer. Funct Integr Genomics 19:311–327. https://doi.org/10.1007/s10142-018-0641-9
Tong W, Yu J, Hou Y et al (2018) Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis). Planta 248:1417–1429. https://doi.org/10.1007/s00425-018-2983-x
Wang PL, Yun B, Muh Ching Y et al (2014) Circular RNA is expressed across the eukaryotic tree of life. PLoS ONE 9:e90859. https://doi.org/10.1371/journal.pone.0090859
Wang WH, Wang JL, Wei QZ, et al (2019a) 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. Sci Rep 9: 14544. https://doi.org/10.1038/s41598-019-51190-0
Wang XS, Chang XC, Jing Y et al (2020) Identification and functional prediction of soybean CircRNAs involved in low-temperature responses. J Plant Physiol 250:153188. https://doi.org/10.1016/j.jplph.2020.153188
Wang YX, Yang M, Wei SM, Qin FJ, Zhao HJ (2017a) Identification of circular RNAs and their targets in leaves of Triticum aestivum L. under dehydration stress. Front Plant Sci 7:2024. https://doi.org/10.3389/fpls.2016.02024
Wang YS, Gao YB, Zhang HX et al (2019b) Genome-wide profiling of circular RNAs in the rapidly growing shoots of Moso Bamboo (Phyllostachys edulis). Plant Cell Physiol 60(6):1354–1373. https://doi.org/10.1093/pcp/pcz043
Wang ZP, Liu YF, Li DW, Li L, Zhang Q, Wang SB, Huang HW (2017b) Identification of circular RNAs in kiwifruit and their species-specific response to bacterial canker pathogen invasion. Front Plant Sci 8:413. https://doi.org/10.3389/fpls.2017.00413
Wu ZH, Huang W, Qin E et al (2020) Comprehensive identification and expression profiling of circular RNAs during nodule development in Phaseolus vulgaris. Front Plant Sci 11:587185. https://doi.org/10.3389/fpls.2020.587185
Yang ZC, Yang Z, Xie YG et al (2020) Systematic identification and analysis of light-responsive circular RNA and co-expression networks in lettuce (Lactuca sativa). G3-GENES GENOM GENET 10:2397–2410. https://doi.org/10.1534/g3.120.401331
Ye C-Y, Chen L, Liu C et al (2015) Widespread noncoding circular RNAs in plants. New Phytol 208:88–95. https://doi.org/10.1111/nph.13585
Zhao R, Li FQ, Tian LL et al (2018) Comprehensive analysis of the whole coding and non-coding RNA transcriptome expression profiles and construction of the circRNA–lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma. Funct Integr Genomics 19:1–13. https://doi.org/10.1007/s10142-018-0631-y
Zhao W, Cheng Y, Zhang C et al (2017) Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean. Sci Rep 7:5636. https://doi.org/10.1038/s41598-017-05922-9
Zhao W, Zhang C, Shen XJ et al (2017) Characterization of circRNAs associated with resistance to defoliating Insects in soybean. Oil Crop Sci 2:23–37. https://doi.org/10.3969/j.issn.2096-2428.2017.01.003
Zhang GY, Diao SF, Zhang T et al (2019) Identification and characterization of circular RNAs during the sea buckthorn fruit development. RNA Biol 16(3):354–361. https://doi.org/10.1080/15476286.2019.1574162
Zhang P, Fan Y, Sun X, Chen L et al (2019) A large scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis. Plant J 98:697–713. https://doi.org/10.1111/tpj.14267
Zhang XO, Dong R, Zhang Y, et al (2016) Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res 26:1277–1287. http://www.genome.org/cgi/doi/10.1101/gr.202895.115
Zhang XO, Wang HB, Zhang Y et al (2014) Complementary sequence-mediated exon circularization. Cell 159:134–147. https://doi.org/10.1016/j.cell.2014.09.001
Zhang XG, Ma XL, Ning LL, et al (2019). Genome-wide identification of circular RNAs in peanut (Arachis hypogaea, L.). BMC Genomics 20:653. https://doi.org/10.1186/s12864-019-6020-7
Acknowledgements
We thank Robert McKenzie, PhD, from Liwen Bianji, Edanz Editing China (www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript.
Funding
This work was partially supported by the Department of Science and Technology of Jilin Province (no. 20180101266JC) and the 13th Five-Year Plan of Science and Technology Project of Jilin (grant no. JJKH20180641KJ).
Author information
Authors and Affiliations
Contributions
Conceptualization: MB. Formal analysis: LZ, WL. Data: HH, ZA, YW, LZ. Methodology: YD, ZJ, GS. Investigation: MB, ZQ, LS, QJ. Validation: MB, YW, LM. Funding acquisition: YD, LZ. Writing original draft: MB. Writing review and editing: MB, YD, ZJ. All authors have read and approved the final manuscript.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Ma, B., Liu, Z., Yan, W. et al. Circular RNAs acting as ceRNAs mediated by miRNAs may be involved in the synthesis of soybean fatty acids. Funct Integr Genomics 21, 435–450 (2021). https://doi.org/10.1007/s10142-021-00791-y
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10142-021-00791-y