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Transcriptomic analysis of Asiatic lily in the process of vernalization via RNA-seq

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Abstract

The new transcriptomes provided comprehensive sequence profiling data of transcriptomic variation during vernalization in Lily Asiatic Hybrids ‘Tiny ghost’. A number of 52,277,184 sequencing raw reads totaling 5.11 Gbp of the chilling treatment (4 °C) sample and 39,466,176 sequencing raw reads totaling 3.85 Gbp of room temperature control (25 °C) sample were assembled de novo into 68,718 unigenes with a mean length of 984 bp, and a total of 33,208 (45.6 %) unigenes were annotated by using public protein databases with a cut-off E value about 10−5. There are 6,153 unigenes of which were assigned to specific metabolic pathways by the Kyoto encyclopedia of genes and genomes. Gene Ontology analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with signal transduction mechanisms, posttranslational modification, protein turnover and chaperones. In addition, the genes expression levels were compared just after vernalization completion between the cold treatment and room temperature control. There are 68,116 unigenes were differentially expressed, and hierarchical clustering analysis arranged 7,301 significantly differentially-expressed unigenes into 56 groups. Six genes related to the vernalization were selected to confirm their expression levels by using quantitative real-time polymerase chain reaction. Furthermore, typical vernalization unigenes VRN1 and VRN2 were identified, and also some vernalization-associated unigenes, such as CBF, SOC, TaAGL, AP2, LEA, LIM et al. were also annotated in the present study. As for VRN1 and VRN2, their expressions were consistent with some previous related studies. Also, this was the first time the vernalization genes VRN1 and VRN2 were founded in lily. According to the results of the present studies, we predicted that they would play an important role during vernalization in Lily Asiatic Hybrids; these data provided the foundation for the future studies of metabolism during vernalization of Asiatic lily.

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Abbreviations

BLAST:

Basic local alignment search tool

COG:

Cluster of orthologous group Cluster

GO:

Gene Ontology

KEGG:

Kyoto encyclopedia of genes and genomes

NCBI:

National Center for Biotechnology Information

qRT-PCR:

Real-time quantitative reverse transcription polymerase chain reaction

References

  1. Lee IL, Kyong CP, Ye SS, Jae HS, Soon JK, Jong KN, Jong HK, Nam SK (2011) Development of expressed sequence tag derived-simple sequence repeats in the genus Lilium. Genes Genomics 33(6):727–733

    Article  CAS  Google Scholar 

  2. Wang G (2011) Transcriptional analysis of young cotton (Gossypium hirsutum) seedlings under salt stress via Solexa sequencing. PhD Dissertation, Shandong Agricultural University

  3. Liu GQ, Li WS, Zheng PH, Xu T, Chen LJ, Liu DF, Hussain S, Teng YW (2012) Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia ear group) buds during the dormancy by NA-Seq. BMC Genomics 13:700–718

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Huang H (2012) The molecular mechanism of salt response in Chrysanthemum lavandulifolium (Fisch. ex Trautv.) Makino. PhD Dissertation, Beijing Forestry University

  5. Shi WF (2012) Research on the transcriptome of Prunus mume through RNA-Seq. PhD Dissertation, Beijing Forestry University

  6. Zhang JX, Wu KL, Zeng SJ, Jaime ATDdS, Zhao XL, Tian CE, Xia HQ, Duan J (2013) Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development. BMC Genomics 14:279–292

    Article  PubMed Central  PubMed  Google Scholar 

  7. Sung S, He YH, Tifani WE, Tamada Y, Johnson L, Nakahigashi K, Goto K, Steve EJ, Richard MA (2006) Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires like heterochromatin protein 1. Nat Genet (Nat) 38(6):706–710

    Article  CAS  Google Scholar 

  8. Yan L, Loukoianov A, Tranquilili G et al (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Yan L, Loukoianov A, Blechl A et al (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–1644

    Article  CAS  PubMed  Google Scholar 

  10. Yan L, Fu D, Li C (2006) From the cover: the wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci USA 103:19581–19586

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Mcintosha RA, Hart GE, Devos KM et al (1998) Catalogue of gene symbols for wheat. In: Wheat genetics symposium. University of Saskatchewan, Saskatoon, pp 1–236

  12. Dubcovsky J, Lijavetzky D, Appendino L et al (1998) Comparative RFLP mapping of Triticum monococcum genes controlling vernalization requirement. Theor Appl Genet 97:968–975

    Article  CAS  Google Scholar 

  13. Yang Y, Xu BY, Jin ZQ (2003) Cloning and analysis of vernalization-related gene VRN2 in Arabidopsis thaliana. Chin J Trop Crops 24:46–50

    Google Scholar 

  14. Michaelsd A (1999) Flowering locus encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11:949–956

    Article  Google Scholar 

  15. Sheldon C, Burn E, Perez P et al (1999) The FLC MADS box gene are pressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11:445–458

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Danyluk J, Kane NA, Breton G, Limin AE, Fowler DB, Sarhan F (2003) TaVRT-1, a putative transcription factor associated with vegetative to reproductive transition in Cereals. Plant Physiol 132(4):1849–1860

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Law CN, Wolfe MS (1966) Location of genetic factors for mildew resistance and ear emergence time on chromosome 7B of wheat. Can J Genet Cytol 18:462–470

    Article  Google Scholar 

  18. Gonch AP (2003) Genetics of growth habit (spring vs winter) in common wheat: confirmation of the existence of dominant gene Vrn4. Theor Appl Genet 107:768–772

    Article  Google Scholar 

  19. Wang XL, Chen W, Li WC, Wu JH, Liu XX, Yang YC (2009) Cloning and characterization of vernalization gene FaVRN1 from Tall Fescue. J Nucl Agric Sci 23(5):778–784

    CAS  Google Scholar 

  20. Zhang WH, Hong LP, Zeng BY (2011) Cloning vernalization-related gene VRN2 and construction of its plant expression vector in Arabidopsis thaliana subtropical. Plant Sci 40(1):1–4

    Article  Google Scholar 

  21. Liu LN, Liu W, Ye QS (2003) Advances on research of vernalization-related gene FLC. Acta Bot Boreal Occident Sin 23(12):2229–2234

    CAS  Google Scholar 

  22. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628

    Article  CAS  PubMed  Google Scholar 

  23. Lister R, Gregory BD, Ecker JR (2009) Next is now: new technologies for sequencing of genomes, trancriptomes, and beyond. Curr Opin Plant Biol 12:107–118

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Marguerat S, Bähler J (2010) RNA-seq: from technology to biology. Cell Mol Life Sci 67:569–579

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Wilhelm BT, Landry JR (2009) RNA-Seq-quantitative measurement of expression through massively parallel RNA-Sequencing. Methods 48:249–257

    Article  CAS  PubMed  Google Scholar 

  26. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144(1):32–42

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Wall PK, Leebens MJ, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, de Pamphilis CW (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10:347

    Article  PubMed Central  PubMed  Google Scholar 

  30. Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G (2010) An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J 63:86–99

    CAS  PubMed  Google Scholar 

  31. Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC (2010) RNA-Seq atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10:160

    Article  PubMed Central  PubMed  Google Scholar 

  32. Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Li W, Huang X, Han B (2010) Functional annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res 20:1238–1249

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51(5):910–918

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Cheung F, Haas BJ, Goldberg SMD, May GD, Xiao Y, Town CD (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7:272

    Article  PubMed Central  PubMed  Google Scholar 

  35. Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9:312

    Article  PubMed Central  PubMed  Google Scholar 

  36. Bellin D, Ferrarini A, Chimento A, Kaiser O, Levenkova N, Bouffard P, Delledonne M (2009) Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species. BMC Genomics 10:555

    Article  PubMed Central  PubMed  Google Scholar 

  37. Collins LJ, Biggs PJ, Voelckel C, Joly S (2008) An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Inform 21:3–14

    Article  CAS  PubMed  Google Scholar 

  38. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  39. Iseli C, Jongeneel C, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1:134–148

    Google Scholar 

  40. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) BLAST2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  41. de Hoon MJL, Imoto S, Nolan J, Miyano S (2004) Open source clustering software. Bioinformatics 20(9):1453–1454

    Article  PubMed  Google Scholar 

  42. Saldanha AJ (2004) Java Treeview—extensible visualization of microarray data. Bioinformatics 20(17):3246–3248

    Article  CAS  PubMed  Google Scholar 

  43. Okoniewski M, Miller C (2006) Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinform 7(1):276

    Article  Google Scholar 

  44. Royce TE, Rozowsky JS, Gerstein MB (2007) Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res 35(15):99

    Article  Google Scholar 

  45. Gendall AR, Levy YY, Wilson A, Dean C (2001) The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis. Cell 107:525–535

    Article  CAS  PubMed  Google Scholar 

  46. Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Lett Nat 427:164–167

    Article  CAS  Google Scholar 

  47. Simpson GG, Dean C (2002) Arabidopsis, the Rosetta stone of flowering time. Science 296:285–289

    Article  CAS  PubMed  Google Scholar 

  48. Parcy F (2005) Flowering: a time for integration. Int J Dev Biol 49:585–593

    Article  PubMed  Google Scholar 

  49. Lee H, Suh SS, Park E, Cho E, Ahn JH, Kim SG, Lee JS, Kwon YM, Lee I (2000) The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis. Genes Dev 14:2366–2376

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  50. Lee S, Kim J, Han JJ, Han MJ, An G (2004) Functional analyses of the flowering time gene OsMADS50, the putative SUPPRESSOR OF OVEREXPRESSION OF CO 1/AGAMOUS-LIKE 20(SOC1/AGL20)ortholog in rice. Plant J 38:754–764

    Article  CAS  PubMed  Google Scholar 

  51. Lee J, Oh M, Park H, Lee I (2008) SOC1 translocated to the nucleus by interaction with AGL24 directly regulates LEAFY. Plant J 55:832–843

    Article  CAS  PubMed  Google Scholar 

  52. Cseke LJ, Zheng J, Podila GK (2003) Characterization of PTM5 in aspen trees: a MADS-box gene expressed during woody vascular development. Gene 318:55–67

    Article  CAS  PubMed  Google Scholar 

  53. Ferrario S, Busscher J, Franken J, Gerats T, Vandenbussche M, Angenent GC, Immink RGH (2004) Ectopic expression of the petunia MADS-box gene UNSHAVEN accelerates flowering and confers leaf-like characteristics to floral organs in a dominant negative manner. Plant Cell 16:1490–1505

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  54. Nakamura T, Song IJ, Fukuda T, Yokoyama J, Maki M, Ochiai T, Kameya T, Kanno A (2005) Characterization of TrcMADS1 gene of Trillium camtschatcense (Trilliaceae) reveals functional evolution of the SOC1/TM3-like gene family. J Plant Res 118:229–234

    Article  CAS  PubMed  Google Scholar 

  55. Zhong XF, Dai X, Xv J, Wu HY, Liu B, Li HY (2012) Cloning and expression analysis of GmGAL1, SOC1 homolog gene in soybean. Mol Biol Rep 9(6):6967–6974

    Article  Google Scholar 

  56. Tan FC, Swain SM (2007) Functional characterization of AP3, SOC1 and WUS homologues from citrus (Citrus sinensis). Physiol Plant 131:481–495

    Article  CAS  PubMed  Google Scholar 

  57. Zhang CH, Liu H, Yu ML, Ge AJ, Dong QH (2011) Bioinformatics analysis of the NAC gene family in strawberry. Jiyinzuxue Yu Yingyong Shengwuxue (Genomics Appl Biol) 30(41):1261–1271

    Google Scholar 

  58. Zhang CH, Shangguan LF, Yu ML, Zhang YP, Ma RJ (2012) Bioinformatics analysis of NAC gene family in peach. Jiangsu J Agric Sci 28(2):406–414

    Google Scholar 

  59. Yaron YL, Caroline D (1998) The transition to flowering. Plant Cell 10:1973–1990

    Article  Google Scholar 

  60. Srikanth A, Schmid M (2011) Regulation of flowering time: all roads lead to Rome. Cell Mol Life Sci 68:2013–2037

    Article  CAS  PubMed  Google Scholar 

  61. Jung C, Muller AE (2009) Flowering time control and applications in plant breeding. Trends Plants Sci 14(10):563–573

    Article  CAS  Google Scholar 

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Acknowledgments

This work was supported by the China National Natural Science Foundation (Grant numbers 31071815 and 31272204), ‘863’ research program (Grant number 2011AA10020804), and the D. Programs Foundation of the Ministry of Education of China (Grant number 20110014110006). Xiaohua Liu and Huang Jie contributed equally to this work.

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Authors and Affiliations

  1. College of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, People’s Republic of China

    Jie Huang, Xiaohua Liu, Jingmao Wang & Yingmin Lü

  2. China National Engineering Research Center for Floriculture, Beijing, 100083, People’s Republic of China

    Jie Huang, Xiaohua Liu, Jingmao Wang & Yingmin Lü

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  1. Jie Huang
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  2. Xiaohua Liu
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  3. Jingmao Wang
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Correspondence to Yingmin Lü.

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Huang, J., Liu, X., Wang, J. et al. Transcriptomic analysis of Asiatic lily in the process of vernalization via RNA-seq. Mol Biol Rep 41, 3839–3852 (2014). https://doi.org/10.1007/s11033-014-3250-2

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  • DOI: https://doi.org/10.1007/s11033-014-3250-2

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