Skip to main content
SpringerLink
Log in

Identification and characterization of microRNAs at different flowering developmental stages in moso bamboo (Phyllostachys edulis) by high-throughput sequencing

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

An Erratum to this article was published on 05 October 2015

Abstract

Researching moso bamboo flowering has been difficult because of its unknown flowering interval and the rarity of florescent samples. To identify microRNAs (miRNAs) and study their expression patterns during the flower developmental process of moso bamboo, small RNAs from non-flowering leaves and four flower developmental periods were sequenced using Illumina technology. In total, 409 known miRNAs and 492 differentially expressed novel miRNAs were identified in moso bamboo. Of the known miRNAs that were differentially expressed between non-flowering and flowering samples, 64 were predicted to have a total of 308 targets. Among the miRNAs, seven known and five novel miRNAs were selected, as were four of their target genes, and their expression profiles were validated using qRT-PCR. The results indicated that the miRNA expression levels were negatively correlated with those of their targets. The research comprehensively revealed that the differentially expressed miRNAs and their targets participated in diverse biological pathways and played significant regulatory roles in moso bamboo flowering. The data provide a significant resource for understanding the molecular mechanisms in moso bamboo flowering and senescence, and serve as the primary foundation for further studies on metabolic regulatory networks that involve miRNAs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Abbreviations

ARF:

Auxin response factor

GAMYB:

Gibberellin MYB gene

GO:

Gene Ontology

GH3:

Gretchen Hagen3

HD-ZIPIII:

Homeodomain-leucine zipperIII

MADS-box:

The initials of MCMl, AGAMOUS, DEFICIENS and SRF 4

MFE:

Minimum free energy

mRNA:

Messenger RNA

miRNAs:

microRNAs

NAC:

NAM, ATAF1/2 and CUC2 domain-containing transcription factors

qRT-PCR:

Quantitative real-time RT-PCR

siRNA:

Small interfering RNA

SPL:

Squamosa promoter binding protein-like

snoRNA:

Small nucleolar RNA

snRNA:

Small nuclear RNA

sRNA:

Small RNA

TIP41:

Tonoplast intrinsic protein 41

References

  • Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121(2):207–221

    Article  CAS  PubMed  Google Scholar 

  • Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE, Depamphilis CW (2007) Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. Plant J 51(6):991–1003

    Article  CAS  PubMed  Google Scholar 

  • Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A (2013) Rfam. p. 11.0: 10 years of RNA families. Nucleic Acids Res 41:D226–232

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bushati N, Cohen SM (2007) MicroRNA functions. Annu Rev Cell Dev Biol 23:175–205

    Article  CAS  PubMed  Google Scholar 

  • Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem–loop RT–PCR. Nucleic Acids Res 33:e179

    Article  PubMed Central  PubMed  Google Scholar 

  • Chitwood DH, Nogueira FTS, Howell MD, Montgomery TA, Carrington JC, Timmermans MCP (2009) Pattern formation via small RNA mobility. Genes Dev 23:549–554

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Czech B, Hannon GJ (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet 12:19–31

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ding Y, Chen Z, Zhu C (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot 62:3563–3573

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Duan K, Luo YH, Luo D, Xu ZH, Xue HW (2005) New insights into the complex and coordinated transcriptional regulation networks underlying rice seed development through cDNA chip-based analysis. Plant Mol Biol 57:785–804

    Article  CAS  PubMed  Google Scholar 

  • Fabio F, Amaury DM, George C (2010) SnapShot: Control of flowering in Arabidopsis. Cell 141(3):550

    Article  Google Scholar 

  • Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2:e219

    Article  PubMed Central  PubMed  Google Scholar 

  • Fan CJ, Ma JM, Guo QR, Li XT, Wang H, Lu MZ (2013) Selection of reference genes for quantitative real-time PCR in bamboo (Phyllostachys edulis). PLoS One 8(2):e56573

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gao J, Zhang Y, Zhang CL, Qi FY, Li XP, Mu SH, Peng ZH (2014) Characterization of the floral transcriptome of moso bamboo (Phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-Seq analysis. PLoS One 9:e98910

    Article  PubMed Central  PubMed  Google Scholar 

  • Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C (2010) Systematic comparison of microarray profiling, realtime PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16(5):991–1006

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 17:1376–1386

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Herold A (1980) Regulation of photosynthesis by sink activity-the missing link. New Phytol 86:131–144

    Article  CAS  Google Scholar 

  • Janzen DH (1976) Why bamboos wait so long to flower? Ann Rev Ecol Syst 7:347–391

    Article  Google Scholar 

  • Ji L, Liu X, Yan J, Wang W, Yumul RE, Kim YJ, Dinh TT, Liu J, Cui X, Zheng B, Agarwal M, Liu C, Cao X, Tang G, Chen X (2011) ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis. PLoS Genet 7:e1001358

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jiang ZH (2002) World bamboo and rattan. Liaoning Science and Technology Publishing House, Shenyang

    Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  PubMed  Google Scholar 

  • Jung JH, Park CM (2007) MIR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and floral development in Arabidopsis. Planta 225(6):1327–1338

    Article  CAS  PubMed  Google Scholar 

  • Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115(2):209–216

    Article  CAS  PubMed  Google Scholar 

  • Kim J, Jung JH, Reyes JL, Kim YS, Kim SY, Chung KS, Kim JA, Lee M, Lee Y, Kim VN, Chua NH (2005) microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J 42(1):84–94

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Klein J, Saedler H, Huijser P (1996) A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol Gen Genet 250(1):7–16

    CAS  PubMed  Google Scholar 

  • Lan Y, Su N, Shen Y, Zhang R, Wu F, Cheng Z, Wang J, Zhang X, Guo X, Lei C, Wang J, Jiang L, Mao L, Wan J (2012) Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice. BMC Genom 13:264

    Article  CAS  Google Scholar 

  • Li JH, Yue JJ, Li HT (2012) Evaluation of economic and ecosystem services of moso bamboo stands. Xiandai Horticulture 18:6–7

    CAS  Google Scholar 

  • Licausi F, Weits DA, Pant BD, Scheible WR, Geigenberger P, van Dongen JT (2011) Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability. New Phytol 190:442–456

    Article  CAS  PubMed  Google Scholar 

  • Lim PO, Lee IC, Kim J, Kim HJ, Ryu JS, Woo HR, Nam HG (2010) Auxin response factor 2 (ARF2) plays a major role in regulating auxin-mediated leaf longevity. J Exp Bot 61:1419–1430

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lin SY, Mao GX (2007) The habit and regeneration of bamboo flowering. Forestr Sci Technol 32(5):23–26

    CAS  Google Scholar 

  • Lin XC, Yuan XL, Lin R, Lou YF, Fang W (2012) Morphogenesis of indefinite inflorescence of Phyllostachys violascens (Carr.) A. et Riv. J Fujian College Forestr 32(2):141–145

    Google Scholar 

  • Liu X, Huang J, Wang Y, Khanna K, Xie Z, Owen HA, Zhao D (2010) The role of floral organs in carpels, an Arabidopsis loss-of-function mutation in MicroRNA160a, in organogenesis and the mechanism regulating its expression. Plant J 62:416–428

    Article  PubMed  Google Scholar 

  • Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher SR, Maher C, Zhang L, Ware D, Liu B, Cao X, Meyers BC, Green PJ (2008) Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci USA 105:4951–4956

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mallory AC, Dugas DV, Bartel DP, Bartel B (2004) MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol 14(12):1035–1046

    Article  CAS  PubMed  Google Scholar 

  • Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG (2006) MicroRNA promoter element discovery in Arabidopsis. RNA 12(9):1612–1619

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Jones SG, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu J (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20:3186–3190

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133:116–127

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Morin RD, O’Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18:610–621

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nag A, Jack T (2010) Sculpting the flower; the role of microRNAs in flower development. Curr Top Dev Biol 91:349–378

    Article  CAS  PubMed  Google Scholar 

  • Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker JR, Reed JW (2005) Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development 132(18):4107–4118

    Article  CAS  PubMed  Google Scholar 

  • Nobuta K, Venu R, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ, Wang G (2007) An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25:473–477

    Article  CAS  PubMed  Google Scholar 

  • Nogueira FTS, Madi S, Chitwood DH, Juarez MT, Timmermans MCP (2007) Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev 21:750–755

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Okawa S, Makino A, Mae T (2003) Effect of irradiance on the partitioning of assimilated carbon during the early phase of grain filling in rice. Ann Bot 92:357–364

    Article  PubMed Central  PubMed  Google Scholar 

  • Parizotto EA, Dunoyer P, Rahm N, Himber C, Voinnet O (2004) In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes Dev 18(18):2237–2242

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Park CM (2005) microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J 42(1):84–94

    Article  PubMed Central  PubMed  Google Scholar 

  • Pelaez P, Trejo SM, Lniguez PL, Navarrete EG, Covarrubias AA, Reyes LJ, Sanchez F (2012) Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genom 13:83

    Article  CAS  Google Scholar 

  • Peng ZH, Lu Y, Li LB, Zhao Q, Feng Q, Gao ZM, Lu HY, Hu T, Yao N, Liu KY, Li Y, Fan DL, Guo YL, Li WJ, Lu YQ, Weng QJ, Zhou CC, Zhang L, Huang T, Zhao Y, Zhu CR, Liu XG, Yang XW, Wang T, Miao K, Zhuang CY, Cao XL, Tang WL, Liu GS, Liu YL, Chen J, Liu ZJ, Yuan LC, Liu ZH, Huang XH, Lu TT, Fei BH, Ning ZM, Han B, Jiang ZH (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 45(5):456–461

    Article  CAS  PubMed  Google Scholar 

  • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Development 20:3407–3425

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes. Development 16:1616–1626

    CAS  Google Scholar 

  • Rubio-Somoza I, Cuperus JT, Weigel D, Carrington JC (2009) Regulation and functional specialization of small RNA-target nodes during plant development. Curr Opin Plant Biol 12(5):622–627

    Article  CAS  PubMed  Google Scholar 

  • Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510

    Article  CAS  PubMed  Google Scholar 

  • Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8(4):517–527

    Article  CAS  PubMed  Google Scholar 

  • Shukla LI, Chinnusamy V, Sunkar R (2008) The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochimica et Biophysica Acta—Gene Regul Mech 1779(11):1874–1939

    Google Scholar 

  • Simpson GG, Dean C (2002) Arabidopsis, the rosetta stone of flowering time? Science 296:285–289

    Article  CAS  PubMed  Google Scholar 

  • Song QX, Liu YF, Hu XF, Zhang WK, Ma B, Chen SY, Zhang JS (2011) Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol 11:5

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sun Y, Tan XF, Luo M, Li JA (2014) The sequencing analysis of transcriptome of Vernicia fordii flower buds at two development stages. Scientia Silvae Sinicae 50(5):70–74

    CAS  Google Scholar 

  • Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sunkar R, Girke T, Jain PK, Zhu JK (2005) Cloning and characterization of microRNAs from rice. Plant Cell 17:1397–1411

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MPS, Moulton V, Dalmay T (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genom 9:593

    Article  Google Scholar 

  • Takada S, Hibara KI, Ishida T, Tasaka M (2001) The CUP-SHAPED COTYLEDONI gene of Arabidopsis regulates shoot apical meristem formation. Development 128:1127–1135

    CAS  PubMed  Google Scholar 

  • Unver T, Budak H (2009) Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 230:659–669

    Article  CAS  PubMed  Google Scholar 

  • Valoczi A, Varallyay E, Kauppinen S, Burgyan J, Havelda Z (2006) Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues. Plant J 47(1):140–151

    Article  CAS  PubMed  Google Scholar 

  • Wang JW, Czech B, Weigel D (2009) miR156-Regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 138:738–749

    Article  CAS  PubMed  Google Scholar 

  • Wang L, Hua D, He J, Duan Y, Chen Z, Hong X, Gong Z (2011a) Auxin Response Factor2 (ARF2) and its regulated homeodomain gene HB33 mediate abscisic acid response in Arabidopsis. PLoS Genet 7:e1002172

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wang T, Chen L, Zhao M, Tian Q, Zhang WH (2011b) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high throughput sequencing. BMC Genom 12:367

    Article  CAS  Google Scholar 

  • Williams L, Grigg SP, Xie M, Christensen S, Fletcher JC (2005) Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166 g and its AtHD-ZIP target genes. Development 132:3657–3668

    Article  CAS  PubMed  Google Scholar 

  • Wu MF, Tian Q, Reed JW (2006) Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133:4211–4218

    Article  CAS  PubMed  Google Scholar 

  • Wu G, Park MY, Conway SR, Wang JW, Weigel D, Poethig RS (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138(4):750–759

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Xu M, Liu Q, Nisbet AJ, Cai X, Yan C, Lin R, Yuan Z, Song H, He X, Zhu X (2010) Identification and characterization of microRNAs in Clonorchis sinensis of human health significance. BMC Genom 11:521

    Article  Google Scholar 

  • Xue LJ, Zhang JJ, Xue HW (2009) Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res 37:916–930

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yin ZJ, Shen FF (2010) Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum). Genet Mol Res 9:1186–1196

    Article  CAS  PubMed  Google Scholar 

  • Yu S, Galvao CV, Zhang YC, Horrer D, Zhang TQ, Hao YH, Feng YQ, Wang S, Markus S, Wang JW (2012) Gibberellin regulates the Arabidopsis floral transition through miR156-Targeted SQUAMOSA PROMOTER BINDING–LIKE transcription factors. Plant Cell 24(8):3320–3332

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhan AJ, Li ZH (2007) The nutrition dynamic of N, P, K in umbrella bamboo (Fargesia murielae) before and after flowering. J Wuhan Bot Res 25(2):213–216

    Google Scholar 

  • Zhang B, Pan X, Wang Q, Cobb GP, Anderson TA (2006) Computational identification of microRNAs and their targets. Comput Biol Chem 30(6):395–407

    Article  CAS  PubMed  Google Scholar 

  • Zheng YS, Gao PJ, Chen LG (2003) A study on the physiological and biochemical character of flowering for Dendroclamopsis oldhami. Scientia Silvae Sinicae 39(3):143–147

    Google Scholar 

  • Zhou M, Gu L, Li P, Song X, Wei L, Chen Z, Cao X (2010) Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica). Front Biol 5:67–90

    Article  CAS  Google Scholar 

  • Zhu T, Budworth P, Chen W, Provart N, Chang HS, Guimil S, Su W, Estes B, Zou G, Wang X (2003) Transcriptional control of nutrient partitioning during rice grain filling. Plant Biotechnol J 1:59–70

    Article  CAS  PubMed  Google Scholar 

  • Zhu QH, Spriggs A, Matthew L, Fan LJ, Kennedy G, Gubler F, Helliwell C (2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 18:1456–1465

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This project was supported by the National High Technology Research and Development Program of China “Moso Bamboo Functional Genomics Research” (Grant No. 2013AA102607-4) and the State Forestry Administration ‘948’ project of China (Grant No. 2012-4-49), International Centre for Bamboo and Rattan, China. The authors hope to express their appreciation to the reviewers for this manuscript. This study was funded by the National High Technology Research and Development Program of China “Moso Bamboo Functional Genomics Research” (Grant Number 2013AA102607-4) and the State Forestry Administration ‘948’ project of China (Grant Number 2012-4-49).

Conflict of interest

Jian Gao declares that she has no conflict of interest. Wei Ge declares that he has no conflict of interest. Ying Zhang declares that she has no conflict of interest. Zhanchao Cheng declares that he has no conflict of interest. Long Li declares that he has no conflict of interest. Dan Hou declares that she has no conflict of interest. Chenglin Hou declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Author information

Author notes

    Authors and Affiliations

    1. Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Chaoyang District, 100102, Beijing, People’s Republic of China

      Jian Gao, Wei Ge, Ying Zhang, Zhanchao Cheng, Long Li & Dan Hou

    2. Capital Normal University School of Life Science, No. 105, The Third Ring Road, Haidian District, 100048, Beijing, People’s Republic of China

      Chenglin Hou

    Authors
    1. Jian Gao
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Wei Ge
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Ying Zhang
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Zhanchao Cheng
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Long Li
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Dan Hou
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Chenglin Hou
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Jian Gao.

    Additional information

    Communicated by H. Siomi.

    J. Gao and W. Ge contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary material 1 (PDF 76 kb). Summary of small RNA sequencing data analysis

    438_2015_1069_MOESM2_ESM.jpg

    Supplementary material 2 (JPEG 1359 kb). Sequence length distribution of moso bamboo sRNAs Length distribution in small RNA libraries. Average percentage (Y-axis) of high quality (filled green bars) sequences of 10-44 nt length (X-axis) for each of the four sequenced libraries. A: ck library; B: F-1 library; C: F-2 library; D: F-3 library; E: F-4 library

    Supplementary material 3 (PDF 832 kb). Known miRNAs from moso bamboo

    438_2015_1069_MOESM4_ESM.jpg

    Supplementary material 4 (JPEG 1525 kb). Novel miRNA candidates first nucleotide bias in moso bamboo A: ck library; B: F-1 library; C: F-2 library; D: F-3 library; E: F-4 library

    438_2015_1069_MOESM5_ESM.jpg

    Supplementary material 5 (JPEG 2682 kb). Novel miRNA nucleotide bias at each position in moso bamboo A: ck library; B: F-1 library; C: F-2 library; D: F-3 library; E: F-4 library

    438_2015_1069_MOESM6_ESM.pdf

    Supplementary material 6 (PDF 286 kb). Potential targets of differentially expressed known miRNAs between ck library and F libraries

    438_2015_1069_MOESM7_ESM.jpg

    Supplementary material 7 (JPEG 2067 kb). Gene ontology of the predicted targets for differentially expressed known miRNAs Categorization of miRNA-target genes was performed according to the biological process, cellular component and molecular function. A: Gene ontology of the predicted targets for differentially expressed known miRNAs between F-1 library and ck library. B: Gene ontology of the predicted targets for differentially expressed known miRNAs between F-2 library and ck library. C: Gene ontology of the predicted targets for differentially expressed known miRNAs between F-3 library and ck library. D: Gene ontology of the predicted targets for differentially expressed known miRNAs between F-4 library and ck library

    Supplementary material 8 (DOC 136 kb)

    Supplementary material 9 (DOC 1,281 kb)

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Gao, J., Ge, W., Zhang, Y. et al. Identification and characterization of microRNAs at different flowering developmental stages in moso bamboo (Phyllostachys edulis) by high-throughput sequencing. Mol Genet Genomics 290, 2335–2353 (2015). https://doi.org/10.1007/s00438-015-1069-8

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s00438-015-1069-8

    Keywords

    Search

    Navigation