Screening and characterization of long noncoding RNAs involved in the albinism of Ananas comosus var. bracteatus leaves

Autoři: Zhen Lin aff001;  Yingyuan Xiong aff001;  Yanbin Xue aff001;  Meiqin Mao aff001;  Yixuan Xiang aff001;  Yehua He aff002;  Fatima Rafique aff001;  Hao Hu aff001;  Jiawen Liu aff001;  Xi Li aff001;  Lingxia Sun aff001;  Zhuo Huang aff001;  Jun Ma aff001
Působiště autorů: College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China aff001;  Horticultural Biotechnology College of South China Agricultural University, Guangzhou, Guangdong, China aff002
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0225602


Long noncoding RNAs (lncRNAs) have been reported to play key regulatory roles in plant growth, development, and biotic and abiotic stress physiology. Revealing the mechanism of lncRNA regulation in the albino portions of leaves is important for understanding the development of chimeric leaves in Ananas comosus var. bracteatus. In this study, a total of 3,543 candidate lncRNAs were identified, among which 1,451 were differentially expressed between completely green (CGr) and completely white (CWh) leaves. LncRNAs tend to have shorter transcripts, lower expression levels, and greater expression specificity than protein-coding genes. Predicted lncRNA targets were functionally annotated by the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A lncRNA-mRNA interaction network was constructed, and 36 target mRNAs related to chlorophyll metabolism were predicted to interact with 86 lncRNAs. Among these, 25 significantly differentially expressed lncRNAs putatively interacted with 16 target mRNAs. Based on an expression pattern analysis of the lncRNAs and their target mRNAs, the lncRNAs targeting magnesium chelatase subunit H (ChlH), protochlorophyllide oxidoreductase (POR), and heme o synthase (COX10) were suggested as key regulators of chlorophyll metabolism. This study provides the first lncRNA database for A. comosus var. bracteatus and contributes greatly to understanding the mechanism of epigenetic regulation of leaf albinism.

Klíčová slova:

Alternative splicing – Biosynthesis – Gene expression – Chlorophyll – Leaves – Long non-coding RNAs – Messenger RNA – RNA sequencing


1. Prensner JR, Chinnaiyan AM. The emergence of lncRNAs in cancer biology. Cancer Discovery. 2011; 1: 391–407. doi: 10.1158/2159-8290.CD-11-0209 22096659

2. Ulitsky I. Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nature Reviews Genetics. 2016; 17: 601–614. doi: 10.1038/nrg.2016.85 27573374

3. Necsulea A, Kaessmann H. Evolutionary dynamics of coding and non-coding transcriptomes. Nature Reviews Genetics. 2014; 15: 734–748. doi: 10.1038/nrg3802 25297727

4. Moran VA, Perera RJ, Khalil AM. Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Researchm. 2012; 40: 6391–6400. doi: 10.1093/nar/gks296 22492512

5. Kung JT, Colognori D, Lee JT. Long noncoding RNAs: past, present, and future. Genetics. 2013; 193: 651–669. doi: 10.1534/genetics.112.146704 23463798

6. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nature Reviews Genetics. 2009; 10: 155–159. doi: 10.1038/nrg2521 19188922

7. Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell. 2008; 135: 635–648. doi: 10.1016/j.cell.2008.09.035 19013275

8. Jenkins AM, Waterhouse RM, Muskavitch MA. Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex. Bmc Genomics. 2015; 16: 337. doi: 10.1186/s12864-015-1507-3 25903279

9. Novikova IV, Hennelly SP, Sanbonmatsu KY. Sizing up long non-coding RNAs: Do lncRNAs have secondary and tertiary structure?. Bioarchitecture. 2012; 2: 189–199. doi: 10.4161/bioa.22592 23267412

10. Wang CY, Liu SR, Zhang XY, Ma YJ, Hu CG, Zhang JZ. Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.). Scientific Reports. 2017; 7: 43226. doi: 10.1038/srep43226 28233798

11. Chen LL, Carmichae, GG. Decoding the function of nuclear long noncoding RNAs. Current Opinion in Cell Biology. 2010; 22: 357–364. doi: 10.1016/ 20356723

12. Beckedorff FC, Amaral MS, Deocesanopereira C, Verjovskialmeida S. Long non-coding RNAs and their implications in cancer epigenetics. Bioscience Reports. 2013; 33: 667–675. doi: 10.1042/BSR20130054 23875687

13. Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nature Reviews Genetics. 2014; 15: 7–21. doi: 10.1038/nrg3606 24296535

14. Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nature Genetics. 2011; 43: 621–629. doi: 10.1038/ng.848 21642992

15. Malouf GG, Zhang J, Yuan Y, Compérat E, Rouprêt M, Cussenot O, Chen Y et al. Characterization of long non-coding RNA transcriptome in clear-cell renal cell carcinoma by next-generation deep sequencing. Molecular Oncology. 2015; 9: 32–43. doi: 10.1016/j.molonc.2014.07.007 25126716

16. Gutschner T, Diederichs S. The hallmarks of cancer: a long non-coding RNA point of view. Rna Biology. 2012; 9: 703–719. doi: 10.4161/rna.20481 22664915

17. Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends in Cell Biology. 2011; 21: 354–361. doi: 10.1016/j.tcb.2011.04.001 21550244

18. Li H, Wang Y, Chen M, Xiao P, Hu C, Zeng Z et al. Genome-wide long non-coding RNA screening, identification and characterization in a model microorganism Chlamydomonas reinhardtii. Scientific Reports. 2016; 6: 34109. doi: 10.1038/srep34109 27659799

19. Amor BB, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, Hirsch J, et al. Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Research. 2009; 19: 57–69. doi: 10.1101/gr.080275.108 18997003

20. Hirsch J, Lefort V, Vankersschaver M, Boualem A, Lucas A, Thermes C et al. Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiology. 2006; 140: 1192–1204. doi: 10.1104/pp.105.073817 16500993

21. Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, Yao J et al. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109: 2654–2659. doi: 10.1073/pnas.1121374109 22308482

22. Ma J, Yan B, Qu Y, Qin F, Yang Y, Hao X, et al. Zm401, a short-open reading-frame mRNA or noncoding RNA, is essential for tapetum and microspore development and can regulate the floret formation in maize. Journal of Cellular Biochemistry. 2008; 105: 136–146. doi: 10.1002/jcb.21807 18465785

23. Coppens d’Eeckenbrugge G, Leal F. Morphology, anatomy and taxonomy. In: Bartholomew DP, Paull RE, Rohrbach KG (eds) The pineapple: botany, production and uses. CABI Publishing, Oxon, UK; 2003; pp. 13–32.

24. Ma J, Kanakala S, He Y, Zhang J, Zhong X. Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis. PLoS One. 2015; 10:e0119153. doi: 10.1371/journal.pone.0119153 25769053

25. Collins JL. The Pineapple, Botany, Utilisation, Cultivation. Leonard Hill Ltd, London, UK; 1960.

26. Montinola LR. Pina. Amon Foundation, Manila, Philippines; 1991.

27. Taussig SJ, Batkin S. Bromelain, the enzyme complex of pineapple (Ananas comosus) and its clinical application: an update. J Ethnopharmacol. 1998; 22: 191–203. doi: 10.1016/0378-8741(88)90127-4 3287010

28. Li X, Kanakala S, He Y, Zhong X, Yu S, Li R, et al. Physiological Characterization and Comparative Transcriptome Analysis of White and Green Leaves of Ananas comosus var. bracteatus. Plos One. 2017; 12: e0169838. doi: 10.1371/journal.pone.0169838 28095462

29. Ma J, Kanakala S, He Y, Zhang J, Zhong X. Transcriptome Sequence Analysis of an Ornamental Plant, Ananas comosus var. bracteatus, Revealed the Potential Unigenes Involved in Terpenoid and Phenylpropanoid Biosynthesis. Plos One. 2015; 10: e0119153. doi: 10.1371/journal.pone.0119153 25769053

30. Xiong YY, Ma J, He YH, Lin Z, Li X, Yu SM, et al. High-throughput sequencing analysis revealed the regulation patterns of small RNAs on the development of A. comosus var. bracteatus leaves. Scientific Reports. 2018; 8: 1947. doi: 10.1038/s41598-018-20261-z 29386560

31. 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 Biology. 2013; 14: R36. doi: 10.1186/gb-2013-14-4-r36 23618408

32. Ghosh S, Chan CK. Analysis of RNA-Seq Data Using TopHat and Cufflinks. Methods in Molecular Biology. 2016; 1374: 339–361. doi: 10.1007/978-1-4939-3167-5_18 26519415

33. Florea L, Song L, Salzberg SL. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000 Research. 2013; 2: 188. doi: 10.12688/f1000research.2-188.v2 24555089

34. Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research. 2007; 35: W345–W349. doi: 10.1093/nar/gkm391 17631615

35. Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, et al. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Research. 2013; 41: e166. doi: 10.1093/nar/gkt646 23892401

36. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Research. 2014; 42: 222–30. doi: 10.1093/nar/gkt1223 24288371.

37. Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W, et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Research. 2013; 41: e74–e74. doi: 10.1093/nar/gkt006 23335781

38. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology. 2010; 28: 511–515. doi: 10.1038/nbt.1621 20436464

39. Li J, Ma W, Zeng P, Wang J, Geng B, Yang J, et al. LncTar: a tool for predicting the RNA targets of long noncoding RNAs. Briefings in Bioinformatics. 2015; 16: 806–812. doi: 10.1093/bib/bbu048 25524864

40. Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, et al. EBSeq: an empirical bayes hierarchical model for inference in rna-seq experiments. Bioinformatics. 2013; 29: 1035–1043. doi: 10.1093/bioinformatics/btt087 23428641

41. Alexa A, Rahnenfuhrer J. TopGO: Enrichment analysis for Gene Ontology. R Package Version; 2006.

42. Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research. 2011; 39: 316–22. doi: 10.1093/nar/gkr483 21715386

43. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J. et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research. 2013; 41: 808–815.

44. Brown BM, Wang Z, Brown KR, Cricco JA, Hegg EL. Heme O synthase and heme A synthase from Bacillus subtilis and Rhodobacter sphaeroides interact in Escherichia coli. Biochemistry. 2004; 43: 13541–13548. doi: 10.1021/bi048469k 15491161

45. Mogi T. Over-expression and characterization of Bacillus subtilis heme O synthase. Journal of Biochemistry. 2009; 145: 669–675. doi: 10.1093/jb/mvp024 19204012

46. Walker CJ, Willows RD. Mechanism and regulation of Mg-chelatase. Biochemical Journal. 1997; 327: 321–333. doi: 10.1042/bj3270321 9359397

47. Fodje MN, Hansson A, Hansson M, Olsen JG, Gough S, Willows RD, et al. Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase. Journal of Molecular Biology. 2001; 311: 111–122. doi: 10.1006/jmbi.2001.4834 11469861

48. Quattro C, Enrico Pè M, Bertolini E. Long noncoding RNAs in the model species Brachypodium distachyon. Scientific Reports. 2017; 7: 11252. doi: 10.1038/s41598-017-11206-z 28900227

49. Ariel F, Romero-Barrios N, Jégu T, Benhamed M, Crespi M. Battles and hijacks: noncoding transcription in plants. Trends in Plant Science. 2015; 20: 362–371. doi: 10.1016/j.tplants.2015.03.003 25850611

50. Shafiq S, Li J, Sun Q. Functions of plants long non-coding RNAs. Biochim Biophys Acta. 2016; 1859: 155–162. doi: 10.1016/j.bbagrm.2015.06.009 26112461

51. Wang Z, Liu Y, Li L, Li D, Zhang Q, Guo Y et al. Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes. Scientific Reports. 2017; 7: 4910. doi: 10.1038/s41598-017-05377-y 28687784

52. Liu J, Wang H, Chua NH. Long noncoding RNA transcriptome of plants. Plant Biotechnology Journal. 2015; 13: 319–328. doi: 10.1111/pbi.12336 25615265

53. Henriques R, Wang H, Liu J, Boix M, Huang LF, Chua NH. The antiphasic regulatory module comprising CDF5 and its antisense RNA FLORE links the circadian clock to photoperiodic flowering. New Phytologist. 2017; 216: 854–867. doi: 10.1111/nph.14703 28758689

54. Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L et al. Stress-responsive regulation of long noncoding RNAs' polyadenylation in Oryza sativa. Plant Journal. 2018; 93: 814–827. doi: 10.1111/tpj.13804 29265542

55. Zhou B, Zhao H, Yu J, Guo C, Dou X, Song F, et al. EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Research. 2018; 46: 100–105. doi: 10.1093/nar/gkx677 28985416

56. Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S, et al. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Developmental Cell. 2014; 30: 166–176. doi: 10.1016/j.devcel.2014.06.017 25073154

57. Chekanova JA. Long non-coding RNAs and their functions in plants. Current Opinion in Plant Biology. 2015; 27: 207–216. doi: 10.1016/j.pbi.2015.08.003 26342908

58. Abdel-Ghany SE, Hamilton M, Jacobi JL, Ngam P, Devitt N, Schilkey F,. et al. A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun. 2016; 7: 11706. doi: 10.1038/ncomms11706 27339290

59. Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, et al. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun. 2016; 7: 11708. doi: 10.1038/ncomms11708 27339440

60. Chao Y, Yuan J, Guo T, Xu L, Mu Z, Han L. Analysis of transcripts and splice isoforms in medicago sativa l. by single-molecule long-read sequencing. Plant Molecular Biology. 2019; 119: 1–17. doi: 10.1007/s11103-018-0813-y 30600412

61. Chen Y, Luo YY, Qiu NF, Hu F, Sheng LL, Wang RQ, et al. Ce 3+ induces flavonoids accumulation by regulation of pigments, ions, chlorophyll fluorescence and antioxidant enzymes in suspension cells of Ginkgo biloba L. Plant Cell Tissue and Organ Culture. 2015; 123: 283–296. doi: 10.1007/s11240-015-0831-2

62. Wei Q, Cao HM, Li ZR, Kuai BK, Ding YL. Identification of an AtCRN1-like chloroplast protein BeCRN1 and its distinctive role in chlorophyll breakdown during leaf senescence in bamboo (Bambusa emeiensis ‘Viridiflavus’). Plant Cell Tissue and Organ Culture. 2013; 114: 1–10. doi: 10.1007/s11240-013-0298-y

63. Xu J, Li Y, Wang Y, Liu X, Zhu XG. Altered expression profiles of microRNA families during de-etiolation of maize and rice leaves. BMC Research Notes. 2017; 10: 108. doi: 10.1186/s13104-016-2367-x 28235420

64. Zhu L, Yang Z, Zeng X, Gao J, Liu J, Yi B, et al. Heme oxygenase 1 defects lead to reduced chlorophyll in Brassica napus. Plant Molecular Biology. 2017; 93: 579–592. doi: 10.1007/s11103-017-0583-y 28108964

65. Motohashi R, Ito T, Kobayashi M, Taji T, Nagata N, Asami T, et al. Functional analysis of the 37 kDa inner envelope membrane polypeptide in chloroplast biogenesis using a Ds-tagged Arabidopsis pale-green mutant. Plant Journal. 2003; 34: 719–731. doi: 10.1046/j.1365-313x.2003.01763.x 12787252

66. Sugimoto H, Kusumi K, Tozawa Y, Yazaki J, Kishimoto N, Kikuchi S, et al. The virescent-2 mutation inhibits translation of plastid transcripts for the plastid genetic system at an early stage of chloroplast differentiation. Plant and Cell Physiology. 2004; 45: 985–996. doi: 10.1093/pcp/pch111 15356324

67. Chen G, Bi YR, Li N. EGYl encodes a membrane-associated and ATP-independent metalloprotease that is required for chloroplast development. Plant Journal. 2005; 41: 364–375. doi: 10.1111/j.1365-313X.2004.02308.x 15659096

68. Lin CS, Lai YH, Sun CW, Liu NT, Tsay HS, Chang WH, et al. Identification of ESTs differentially expressed in green and albino mutant bamboo (Bambusa edulis) by suppressive subtractive hybridization (SSH) and microarray analysis. Plant Cell Tissue and Organ Culture. 2006; 86: 169–175. doi: 10.1007/s11240-006-9105-3

69. Okazawa A, Tango L, Itoh Y, Fukusaki E, Kobayashi A. Characterization and subcellular localization of chlorophyllase from Ginkgo biloba. Zeitschrift Fur Naturforschung C A Journal of Biosciences. 2006; 61: 111–117. doi: 10.1515/znc-2006-1-220 16610227

70. Walker CJ, Weinstein JD. In vitro assay of the chlorophyll biosynthetic enzyme Mg-chelatase: resolution of the activity into soluble and membrane-bound fractions. Proceedings of the National Academy of Sciences of the United States of America. 1991; 88: 5789–5793. doi: 10.1073/pnas.88.13.5789 11607197

71. Apel K, Santel HJ, Redlinger TE, Falk H. The protochlorophyllide holochrome of barley (Hordeum vulgare L.). Isolation and characterization of the NADPH:protochlorophyllide oxidoreductase. Eur J Biochem. 1980; 111: 251–258. doi: 10.1111/j.1432-1033.1980.tb06100.x 7439188

72. Masuda T, Takamiya K. Novel insights into the enzymology, regulation and physiological functions of light-dependent protochlorophyllide oxidoreductase in angiosperms. Photosynthesis Research. 2004; 81: 1–29. doi: 10.1023/B:PRES.0000028392.80354.7c 16328844

73. Archipowa N, Kutta RJ, Heyes DJ, Scrutton NS. Stepwise hydride transfer in a biological system: insights into the reaction mechanism of the light‐dependent protochlorophyllide oxidoreductase. Angew. Chem. Int. Ed. Engl. 2018; 57: 2682–2686. doi: 10.1002/anie.201712729 29363234

74. Us-Camas R, Castillo-Castro E, Aguilar-Espinosa M, Limones-Briones V, Rivera-Madrid R, Robert-Díaz ML, et al. Assessment of molecular and epigenetic changes in the albinism of Agave angustifolia Haw. Plant Science. 2017; 263: 156–167. doi: 10.1016/j.plantsci.2017.07.010 28818371

Článek vyšel v časopise


2019 Číslo 11