Abstract
Key message
We identified several novel lncRNAs that play important roles in Ginkgo biloba leaf development.
Abstract
A large number of long non-coding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, lncRNAs and their regulatory roles remain poorly characterized in woody plants, particularly in the gymnosperm G. biloba. We performed deep strand-specific RNA sequencing (ssRNA-seq), and obtained 27.44 GB raw data from all major developmental stages of G. biloba leaves. From these sequencing data, we identified 1323 novel lncRNAs. These lncRNAs were transcribed from 947 scaffolds of G. biloba, 57.6% of which came from intergenic regions. We also confirmed that Gb-lncRNAs were shorter and had fewer exons than protein-coding genes. Target prediction for 764 lncRNAs identified 1184 target genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis revealed that these lncRNAs might be associated with photosynthesis, plant hormones, and secondary metabolism in leaves. Moreover, we constructed a network of regulatory interactions between lncRNAs and mRNAs; 89 lncRNAs were predicted as targets of 64 miRNAs and 33 lncRNAs functioned as miRNA precursors. Quantitative real-time PCR revealed that novel lncRNAs had stage- and tissue-specific expression patterns in G. biloba leaves. These results provide new insight into the function of lncRNAs in leaves and enhance our understanding of plant lncRNAs.
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References
Bo XC, Wang SQ (2004) TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. Bioinformatics 21:1401–1402. https://doi.org/10.1093/bioinformatics/bti211
Chen JH, Quan MY, Zhang DQ (2014) Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq. Planta 241:125–143. https://doi.org/10.1007/s00425-014-2168-1
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149–1154. https://doi.org/10.1126/science.1108625
Di C, Yuan JP, Wu Y, Li JR, Lin HX, Hu L, Zhang T, Qi YJ, Gerstein MB, Guo Y, Lu ZJ (2014) Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J 80:848–861. https://doi.org/10.1111/tpj.12679
Fatica A, Bozzoni I (2013) Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet 15:1–13. https://doi.org/10.1038/nrg3606
Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, García JA, Paz-Ares J (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39:1033–1037. https://doi.org/10.1038/ng2079
Guan R, Zhao YP, Zhang H, Fan GY, Liu X, Zhou WB, Shi CC, Wang JH, Liu WQ, Liang XM, Fu YY, Ma KL, Zhao LJ, Zhang FM, Lu ZH, Lee SMY, Xu X, Wang J, Yang HM, Fu CX, Ge S, Chen WB (2016) Draft genome of the living fossil Ginkgo biloba. GigaScience 5:49. https://doi.org/10.1186/s13742-016-0154-1
He F, Liu QQ, Zheng L, Cui YQ, Shen ZG, Zheng LQ (2015) RNA-Seq analysis of rice roots reveals the involvement of post-transcriptional regulation in response to cadmium stress. Front Plant Sci 6:1136. https://doi.org/10.3389/fpls.2015.01136
Heo JB, Lee YS, Sung S (2013) Epigenetics regulation by long noncoding RNAs in plants. Chromosome Res 21:685–693. https://doi.org/10.1007/s10577-013-9392-6
Ilott NE, Ponting CP (2013) Predicting long non-coding RNAs using RNA sequencing. Methods 63:50–59. https://doi.org/10.1016/j.ymeth.2013.03.019
Kang CY, Liu ZC (2015) Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca, during flower and fruit development. BMC Genom 16:815. https://doi.org/10.1186/s12864-015-2014-2
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
Kornienko AE, Guenzl PM, Barlow DP, Pauler FM (2013) Gene regulation by the act of long non-coding RNA transcription. BMC Biol 11:59. https://doi.org/10.1186/1741-7007-11-59
Laurent GS, Wahlestedt C, Kapranov P (2015) The landscape of long noncoding RNA classification. Trends Genet 31:239–251. https://doi.org/10.1016/j.tig.2015.03.007
Li H, Wang H, Yuan Z, Cao X, Yang Z, Zhang D, Xu Y, Huang H (2005) The putative RNA-dependent RNA polymerase RDR6 acts synergistically with ASYMMETRIC LEAVES1 and 2 to repress BREVIPEDICELLUS and MicroRNA165/166 in Arabidopsis leaf development. Plant Cell 17:2157–2171. https://doi.org/10.1105/tpc.105.033449
Li L, Eichten SR, Shimizu R et al (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol 15:R40. https://doi.org/10.1186/gb-2014-15-2-r40
Li JW, Ma W, Zeng P, Wang JY, Geng B, Yang JC, Cui QG (2015) LncTar: a tool for predicting the RNA targets of long noncoding RNAs. Brief Bioinform 16:806–812. https://doi.org/10.1093/bib/bbu048
Li H, Wang YT, Chen MR, Xiao P, Hu CX, Zeng ZY, Wang CG, Wang JX, Hu ZL (2016) Genome-wide long non-coding RNA screening, identification and characterization in a model microorganism Chlamydomonas reinhardtii. Sci Rep 6:34109. https://doi.org/10.1038/srep34109
Li SX, Yu X, Lei N, Cheng ZH, Zhao PJ, He YK, Wang WQ, Peng M (2017) Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava. Sci Rep 7:46795. https://doi.org/10.1038/srep45981
Li WX, Yang SB, Lu ZG, He ZC, Ye YL, Zhao BB, Wang L, Jin B (2018) Cytological, physiological, and transcriptomic analyses of golden leaf coloration in Ginkgo biloba L. Hortic Res 5:12. https://doi.org/10.1038/s41438-018-0015-4
Lin JK, Wilson IW, Ge GP, Sun GL, Xie FL, Yang YF, Wu LY, Zhang BH, Wu JQ, Zhang Y, Qiu DY (2017) Whole transcriptome analysis of three leaf stages in two cultivars and one of their F1 hybrid of Camellia sinensis L. with differing EGCG content. Tree Genet Genom 13:13. https://doi.org/10.1007/s11295-016-1089-5
Liu DM, Song Y, Chen ZX, Yu DQ (2009) Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiol Plant 136:223–236. https://doi.org/10.1111/j.1399-3054.2009.01229.x
Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua NH (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24:4333–4345. https://doi.org/10.1105/tpc.112.102855
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2–∆∆Ct method. Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Lu ZG, Xia X, Jiang B, Ma KB, Zhu LK, Wang L, Jin B (2017a) Identification and characterization of novel lncRNAs in Arabidopsis thaliana. Biochem Biophys Res Commun 488:348–354. https://doi.org/10.1016/j.bbrc.2017.05.051
Lu ZG, Xu J, Li WX, Zhang L, Cui JW, He QS, Wang L, Jin B (2017b) Transcriptomic analysis reveals mechanisms of sterile and fertile flower differentiation and development in Viburnum macrocephalum f. keteleeri. Front Plant Sci 8:261. https://doi.org/10.3389/fpls.2017.00261
Lv YD, Liang ZK, Ge M, Qi WC, Zhang TF, Lin F, Peng ZH, Zhao H (2016) Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.). BMC Genom 17:350. https://doi.org/10.1186/s12864-016-2650-1
Ma L, Bajic VB, Zhang Z (2013) On the classification of long non-coding RNAs. RNA Biol 10:924–933. https://doi.org/10.4161/rna.24604
Mohanta TK, Occhipinti A, Zebelo SA, Foti M, Fliegmann J, Bossi S, Maffei ME, Bertea CM (2012) Ginkgo biloba responds to herbivory by activating early signaling and direct defenses. PLoS One 7:e32822. https://doi.org/10.1371/journal.pone.0032822
Nystedt B, Street NR, Wetterbom A et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–584. https://doi.org/10.1038/nature12211
Palatnik JF, Wollmann H, Schommer C, Schwab R, Boisbouvier J, Rodriguez R, Warthmann N, Allen E, Dezulian T, Huson D, Carrington JC, Weigel D (2007) Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev Cell 13:115–125. https://doi.org/10.1016/j.devcel.2007.04.012
Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn L, Regev A, Schier AF (2012) Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 22:577–591. https://doi.org/10.1101/gr.133009.111
Pertea M, Kim D, Pertea G, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11:1650–1667. https://doi.org/10.1038/nprot.2016.095
Pulido A, Laufs P (2010) Co-ordination of developmental processes by small RNAs during leaf development. J Exp Bot 61:1277–1291. https://doi.org/10.1093/jxb/erp397
Rowley MJ, Böhmdorfer G, Wierzbicki AT (2013) Analysis of long non-coding RNAs produced by a specialized RNA polymerase in Arabidopsis thaliana. Methods 63:160–169. https://doi.org/10.1016/j.ymeth.2013.05.006
Shuai P, Liang D, Tang S, Zhang ZJ, Ye CY, Su YY, Xia XL, Yin WL (2014) Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J Exp Bot 65:4975–4983. https://doi.org/10.1093/jxb/eru256
Song X, Sun L, Luo HT, Ma QG, Zhao Y, Pei D (2016) Genome-wide identification and characterization of long non-coding RNAs from mulberry (Morus notabilis) RNA-seq data. Genes 7:11. https://doi.org/10.3390/genes7030011
Tian JX, Song YP, Du QZ, Yang XH, Ci D, Chen JH, Xie JB, Li BL, Zhang DQ (2016) Population genomic analysis of gibberellin-responsive long non-coding RNAs in Populus. J Exp Bot 67:2467–2482. https://doi.org/10.1093/jxb/erw057
Ulitsky I (2016) Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nat Rev Genet 17:601–614. https://doi.org/10.1038/nrg.2016.85
Wang H, Niu QW, Wu HW, Liu J, Ye J, Yu N, Chua NH (2015a) Analysis of noncoding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits. Plant J 84:404–416. https://doi.org/10.1111/tpj.13018
Wang L, Zhao JG, Zhang M, Li WX, Luo KG, Lu ZG, Zhang CQ, Jin B (2015b) Identification and characterization of microRNA expression in Ginkgo biloba. Tree Genet Genomes 11:76. https://doi.org/10.1007/s11295-015-0897-3
Wang MZ, Wu B, Chen C, Lu SF (2015c) Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng. J Integr Plant Biol 57:256–270. https://doi.org/10.1111/jipb.12239
Wang TZ, Liu M, Zhao MG, Chen RJ, Zhang WH (2015d) Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula, using genome-wide high-throughput sequencing. BMC Plant Biol 15:1–13. https://doi.org/10.1186/s12870-015-0530-5
Wang L, Lu ZG, Li W, Xu J, Luo K, Lu W, Jin B (2016a) Global comparative analysis of expressed genes in ovules and leaves of Ginkgo biloba L. Tree Genet Genom 12:1–18. https://doi.org/10.1007/s11295-016-0989-8
Wang L, Zhao JG, Luo KG, Cui JW, He QS, Xia X, Lu ZG, Li WX, Jin B (2016b) Deep sequencing discovery and profiling of conserved and novel miRNAs in the ovule of Ginkgo biloba. Trees 30:1557–1567. https://doi.org/10.1007/s00468-016-1389-2
Wang X, Guo A, Zhang CL, Cui L, Wang JF, Li HX, Zhang JH, Ye ZB (2016c) Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato. New Phytol 209:1442–1455. https://doi.org/10.1111/nph.13718
Wu B, Li Y, Yan HX, Ma YM, Luo HM, Yuan LC, Chen SL, Lu SF (2012) Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC Genom 13:15. https://doi.org/10.1186/1471-2164-13-15
Zhang W, Han ZX, Guo QL, Liu Y, Zheng YX, Wu FL, Jin WB (2014a) Identification of maize long non-coding RNAs responsive to drought stress. PloS One 9:e98958. https://doi.org/10.1371/journal.pone.0098958
Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Chen YQ (2014b) Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol 15:512. https://doi.org/10.1186/s13059-014-0512-1
Zhou DL, Du QZ, Chen JH, Wang QS, Zhang DQ (2017) Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa. DNA Res 24:473–486. https://doi.org/10.1093/dnares/dsx018
Zhu BZ, Yang YF, Li R, Fu D, Wen LW, Luo YB, Zhu HL (2015) RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening. J Exp Bot 66:4483–4495. https://doi.org/10.1093/jxb/erv203
Zhu Y, Chen LX, Zhang CJ, Hao P, Jing XY, Li X (2017) Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii. BMC Genom 18:1042. https://doi.org/10.1186/s12864-016-3266-1
Zou CS, Wang QL, Lu CR, Yang WC, Zhang YP, Cheng HL, Feng XX, Prosper MA, Song G (2016) Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum). Sci China Life 59:164–171. https://doi.org/10.1007/s11427-016-5000-2
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This work was supported financially by National Key R & R Program of China (No. 2017YFD0600701) and Natural Science Foundation of China (Nos. 31670181, 31670695).
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All the raw data from Illumina sequencing and lncRNA transcript information have been deposited in NCBI GEO, under Accession Number GSE109917.
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Communicated by J. Carlson.
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Wang, L., Xia, X., Jiang, H. et al. Genome-wide identification and characterization of novel lncRNAs in Ginkgo biloba. Trees 32, 1429–1442 (2018). https://doi.org/10.1007/s00468-018-1724-x
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DOI: https://doi.org/10.1007/s00468-018-1724-x