Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress

Autoři: Lingling Lv aff001;  Kaiye Yu aff001;  Haiyan Lü aff001;  Xiangqian Zhang aff001;  Xiaoqian Liu aff001;  Chongyuan Sun aff001;  Huanqing Xu aff001;  Jinyu Zhang aff002;  Xiaohui He aff003;  Dan Zhang aff001
Působiště autorů: Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China aff001;  Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China aff002;  Smart City Institute, Zhengzhou University, Zhengzhou, China aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: 10.1371/journal.pone.0227243


Low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Circular RNAs (circRNAs) are novel noncoding RNAs that play a crucial role in plant responses to abiotic stress. However, how LP stress mediates the biogenesis of circRNAs in soybean remains unclear. Here, to explore the response mechanisms of circRNAs to LP stress, the roots of two representative soybean genotypes with different P-use efficiency, Bogao (a LP-sensitive genotype) and Nannong 94156 (a LP-tolerant genotype), were used for the construction of RNA sequencing (RNA-seq) libraries and circRNA identification. In total, 371 novel circRNA candidates, including 120 significantly differentially expressed (DE) circRNAs, were identified across different P levels and genotypes. More DE circRNAs were significantly regulated by LP stress in Bogao than in NN94156, suggesting that the tolerant genotype was less affected by LP stress than the sensitive genotype was; in other words, NN94156 may have a better ability to maintain P homeostasis under LP stress. Moreover, a positive correlation was observed between the expression patterns of P stress-induced circRNAs and their circRNA-host genes. Gene Ontology (GO) enrichment analysis of these circRNA-host genes and microRNA (miRNA)-targeted genes indicated that these DE circRNAs were involved mainly in defense responses, ADP binding, nucleoside binding, organic substance catabolic processes, oxidoreductase activity, and signal transduction. Together, our results revealed that LP stress can significantly alter the genome-wide profiles of circRNAs and indicated that the regulation of circRNAs was both genotype and environment specific in response to LP stress. LP-induced circRNAs might provide a rich resource for LP-responsive circRNA candidates for future studies.

Klíčová slova:

Gene expression – Gene regulation – Long non-coding RNAs – MicroRNAs – Phosphates – Plant resistance to abiotic stress – RNA sequencing – Soybean


1. Scheerer U, Trube N, Netzer F, Rennenberg H, Herschbach C. ATP as phosphorus and nitrogen source for nutrient uptake by fagus sylvatica and populus x canescens roots. Frontiers in Plant Science. 2019;10(378). doi: 10.3389/fpls.2019.00378 31019519

2. Zhang D, Zhang H, Chu S, Li H, Chi Y, Triebwasser-Freese D, et al. Integrating QTL mapping and transcriptomics identifies candidate genes underlying QTLs associated with soybean tolerance to low-phosphorus stress. Plant Molecular Biology. 2017;93(1):137–50. doi: 10.1007/s11103-016-0552-x 27815671

3. Matsui A, Nguyen AH, Nakaminami K, Seki M. Arabidopsis non-coding RNA regulation in abiotic stress responses. International Journal of Molecular Sciences. 2013;14(11):22642–54. doi: 10.3390/ijms141122642 24252906

4. Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su CL. Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell. 2006;18(2):412–21. doi: 10.1105/tpc.105.038943 16387831

5. Li ZX, Zhang XR, Liu XX, Zhao YJ, Wang BM, Zhang JR. miRNA alterations are important mechanism in maize adaptations to low-phosphate environments. Plant Sci. 2016;252:103–17. doi: 10.1016/j.plantsci.2016.07.009 27717445

6. Bao H, Chen H, Chen M, Xu H, Huo X, Xu Q, et al. Transcriptome-wide identification and characterization of microRNAs responsive to phosphate starvation in Populus tomentosa. Functional & integrative genomics. 2019. doi: 10.1007/s10142-019-00692-1 31177404

7. Pant BD, Buhtz A, Kehr J, Scheible W-R. MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant Journal. 2008;53(5):731–8. doi: 10.1111/j.1365-313X.2007.03363.x 17988220

8. Tian L, Liu H, Ren L, Ku L, Wu L, Li M, et al. MicroRNA 399 as a potential integrator of photo-response, phosphate homeostasis, and sucrose signaling under long day condition. Bmc Plant Biology. 2018;18. doi: 10.1186/s12870-018-1460-9 30463514

9. Wang Y, Zhang F, Cui WX, Chen KQ, Zhao R, Zhang ZH. The FvPHR1 transcription factor control phosphate homeostasis by transcriptionally regulating miR399a in woodland strawberry. Plant Science. 2019;280:258–68. doi: 10.1016/j.plantsci.2018.12.025 30824004

10. Hsieh L-C, Lin S-I, Kuo H-F, Chiou T-J. Abundance of tRNA-derived small RNAs in phosphate-starved Arabidopsis roots. Plant signaling & behavior. 2010;5(5):537–9. doi: 10.4161/psb.11029 20404547

11. Hsieh LC, Lin SI, Shih ACC, Chen JW, Lin WY, Tseng CY, et al. Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiology. 2009;151(4):2120–32. doi: 10.1104/pp.109.147280 19854858

12. Shah S, Wittmann S, Kilchert C, Vasiljeva L. IncRNA recruits RNAi and the exosome to dynamically regulate pho1 expression in response to phosphate levels in fission yeast. Genes & Development. 2014;28(3):231–44. doi: 10.1101/gad.230177.113 24493644

13. Garg A, Sanchez AM, Shuman S, Schwer B. A long noncoding (lnc)RNA governs expression of the phosphate transporter Pho84 in fission yeast and has cascading effects on the flanking prt lncRNA and pho1 genes. Journal of Biological Chemistry. 2018;293(12):4456–67. doi: 10.1074/jbc.RA117.001352 29414789

14. Zhang Z, Zheng Y, Ham B-K, Zhang S, Fei Z, Lucas WJ. Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency. Journal of Integrative Plant Biology. 2019;61(4):492–508. doi: 10.1111/jipb.12715 30171742

15. Yuan J, Zhang Y, Dong J, Sun Y, Lim BL, Liu D, et al. Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. Bmc Genomics. 2016;17. doi: 10.1186/s12864-016-2929-2 27538394

16. Wang TZ, Zhao MG, Zhang XX, Liu M, Yang CG, Chen YH, et al. Novel phosphate deficiency-responsive long non-coding RNAs in the legume model plant Medicago truncatula. J Exp Bot. 2017;68(21–22):5937–48. doi: 10.1093/jxb/erx384 29165588

17. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333–8. doi: 10.1038/nature11928 23446348

18. Zhang Y, Zhang XO, Chen T, Xiang JF, Yin QF, Xing YH, et al. Circular Intronic long noncoding RNAs. Mol Cell. 2013;51(6):792–806. doi: 10.1016/j.molcel.2013.08.017 24035497

19. Zhou R, Zhu Y, Zhao J, Fang Z, Wang S, Yin J, et al. Transcriptome-wide identification and characterization of potato circular RNAs in response to pectobacterium carotovorum subspecies brasiliense infection. International Journal of Molecular Sciences. 2018;19(1). doi: 10.3390/ijms19010071 29280973

20. Pan T, Sun X, Liu Y, Li H, Deng G, Lin H, et al. Heat stress alters genome-wide profiles of circular RNAs in Arabidopsis. Plant Molecular Biology. 2018;96(3):217–29. doi: 10.1007/s11103-017-0684-7 29177640

21. Xiang L, Cai C, Cheng J, Wang L, Wu C, Shi Y, et al. Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq. Peer J. 2018;6. doi: 10.7717/peerj.4500 29576969

22. Litholdo CG Jr., da Fonseca GC. Circular RNAs and Plant Stress Responses. In: Xiao J, editor. Circular Rnas: Biogenesis and Functions. Advances in Experimental Medicine and Biology. 10872018. p. 345–53.

23. Ren Y, Yue H, Li L, Xu Y, Wang Z, Xin Z, et al. Identification and characterization of circRNAs involved in the regulation of low nitrogen-promoted root growth in hexaploid wheat. Biological Research. 2018;51. doi: 10.1186/s40659-018-0194-3 30390705

24. Wang K, Wang C, Guo B, Song K, Shi C, Jiang X, et al. CropCircDB: a comprehensive circular RNA resource for crops in response to abiotic stress. Database: the journal of biological databases and curation. 2019;2019. doi: 10.1093/database/baz053 31058278

25. Zhao W, Chu S, Jiao Y. Present Scenario of Circular RNAs (circRNAs) in Plants. Frontiers in Plant Science. 2019;10. doi: 10.3389/fpls.2019.00379 31001302

26. Wang Z, Liu Y, Li D, Li L, Zhang Q, Wang S, et al. Identification of circular RNAs in kiwifruit and their species-specific response to bacterial canker pathogen invasion. Frontiers in Plant Science. 2017;8(413). doi: 10.3389/fpls.2017.00413 28396678

27. Zuo J, Wang Q, Zhu B, Luo Y, Gao L. Deciphering the roles of circRNAs on chilling injury in tomato. Biochemical and Biophysical Research Communications. 2016;479(2):132–8. doi: 10.1016/j.bbrc.2016.07.032 27402275

28. Wang YX, Yang M, Wei SM, Qin FJ, Zhao HJ, Suo B. Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress. Frontiers in Plant Science. 2017;7. doi: 10.3389/fpls.2016.02024 28105043

29. Ye CY, Chen L, Liu C, Zhu QH, Fan LJ. Widespread noncoding circular RNAs in plants. New Phytol. 2015;208(1):88–95. doi: 10.1111/nph.13585 26204923

30. Zhao W, Cheng YH, Zhang C, You QB, Shen XJ, Guo W, et al. Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean. Sci Rep-Uk. 2017;7. doi: 10.1038/s41598-017-05922-9 28717203

31. Andrews S. FastQC: a quality control tool for high throughput sequence data. Available online at: 2010.

32. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. doi: 10.1093/bioinformatics/btu170 24695404

33. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36. doi: 10.1186/gb-2013-14-4-r36 23618408

34. Glazar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. Rna. 2014;20(11):1666–70. doi: 10.1261/rna.043687.113 WOS:000344065900002. 25234927

35. Warnes G, Bolker B, Bonebakker L, Gentleman R, Liaw W, Lumley T, et al. gplots: Various R programming tools for plotting data. R package version. 2009;2(4):1.

36. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods. 2001;25(4):402–8. doi: 10.1006/meth.2001.1262 11846609

37. Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016;26(9):1277–87. doi: 10.1101/gr.202895.115 27365365

38. Gao Y, Wang JF, Zheng Y, Zhang JY, Chen S, Zhao FQ. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nat Commun. 2016;7. doi: 10.1038/ncomms12060 27350239

39. Zhu Y-X, Jia J-H, Yang L, Xia Y-C, Zhang H-L, Jia J-B, et al. Identification of cucumber circular RNAs responsive to salt stress. BMC Plant Biology. 2019;19(1):164. doi: 10.1186/s12870-019-1712-3 31029105

40. Sablok G, Zhao HW, Sun XY. Plant circular RNAs (circRNAs): transcriptional regulation beyond miRNAs in plants. Mol Plant. 2016;9(2):192–4. doi: 10.1016/j.molp.2015.12.021 26774621

41. Herridge DF, Peoples MB, Boddey RM. Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil. 2008;311(1–2):1–18. doi: 10.1007/s11104-008-9668-3

42. Zhang D, Song HN, Cheng H, Hao DR, Wang H, Kan GZ, et al. The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. Plos Genet. 2014;10(1). doi: 10.1371/journal.pgen.1004061 24391523

43. Yin J, Liu M, Ma D, Wu J, Li S, Zhu Y, et al. Identification of circular RNAs and their targets during tomato fruit ripening. Postharvest Biology and Technology. 2018;136:90–8. doi: 10.1016/j.postharvbio.2017.10.013

44. Chiou TJ, Lin SI. Signaling network in sensing phosphate availability in plants. Annu Rev Plant Biol. 2011;62:185–206. doi: 10.1146/annurev-arplant-042110-103849 21370979

45. Veno MT, Hansen TB, Veno ST, Clausen BH, Grebing M, Finsen B, et al. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. Genome biology. 2015;16. doi: 10.1186/s13059-015-0801-3 26541409

46. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495(7441):384–8. doi: 10.1038/nature11993 23446346

47. Du Q, Wang K, Zou C, Xu C, Li W-X. The PILNCR1-miR399 regulatory module is important for low phosphate tolerance in maize. Plant Physiology. 2018;177(4):1743–53. doi: 10.1104/pp.18.00034 29967097

48. Hackenberg M, Shi B-J, Gustafson P, Langridge P. Characterization of phosphorus-regulated miR399 and miR827 and their isomirs in barley under phosphorus-sufficient and phosphorus-deficient conditions. Bmc Plant Biology. 2013;13. doi: 10.1186/1471-2229-13-214 24330740

49. Liu J-Q, Allan DL, Vance CP. Systemic signaling and local sensing of phosphate in common bean: cross-talk between photosynthate and microRNA399. Mol Plant. 2010;3(2):428–37. doi: 10.1093/mp/ssq008 20147371

50. Aung K, Lin S-I, Wu C-C, Huang Y-T, Su C-L, Chiou T-J. pho2, a phosphate overaccumulator, is caused by a nonsense mutation in a MicroRNA399 target gene. Plant Physiology. 2006;141(3):1000–11. doi: 10.1104/pp.106.078063 16679417

51. Chao LI, Sha AHJCJoOCS. Overexpression of Gm mIR319 in tobacco improving tolerance to phosphorus deficiency. Chinese Journal of Oil Crop Sciences. 2016. doi: 10.7505/j.issn.1007-9084.2016.02.005

52. Lei KJ, Lin YM, An GY. miR156 modulates rhizosphere acidification in response to phosphate limitation in Arabidopsis. Journal of Plant Research. 2016;129(2):275–84. doi: 10.1007/s10265-015-0778-8 26659856

53. Li ZY, Xu HY, Li Y, Wan XF, Ma Z, Cao J, et al. Analysis of physiological and miRNA responses to Pi deficiency in alfalfa (Medicago sativa L.). Plant Molecular Biology. 2018;96(4–5):473–92. doi: 10.1007/s11103-018-0711-3 29532290

54. Srivastava S, Srivastava AK, Suprasanna P, D'Souza SFJJoEB. Identification and profiling of arsenic stress-induced microRNAs in Brassica juncea. J Exp Bot. 2013;64(1):303–15. doi: 10.1093/jxb/ers333 23162117

55. Khaldun ABM, Huang W, Lv H, Liao S, Zeng S, Wang Y. Comparative profiling of miRNAs and target gene identification in distant-grafting between tomato and lycium (Goji Berry). Frontiers in Plant Science. 2016;7. doi: 10.3389/fpls.2016.01475 27803702

56. Zhao WL, Liang DL, Shi M, Bin HU, Xiao R, Wang JW. Effects of phosphate and selenate interactions on uptake of phosphorus and selenium by Pak Choi. Journal of Agro-Environment Science. 2013;32(12):2331–8. doi: 10.11654/jaes.2013.12.004

57. Liu Q, Wang DJ, Jiang XJ, Cao ZH, Health. Effects of the interactions between selenium and phosphorus on the growth and selenium accumulation in rice (Oryza Sativa). J Environmental Geochemistry. 2004;26(2):325–30. doi: 10.1023/B:EGAH.0000039597.75201.57

58. Takken FLW, Albrecht M, Tameling WIL. Resistance proteins: molecular switches of plant defence. Curr Opin Plant Biol. 2006;9(4):383–90. doi: 10.1016/j.pbi.2006.05.009 16713729

59. Chen WJ, Zhu TJTiPS. Networks of transcription factors with roles in environmental stress response. Trends in Plant Science. 2004;9(12):591–6. doi: 10.1016/j.tplants.2004.10.007 15564126

Článek vyšel v časopise


2020 Číslo 1