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RNA-Seq analysis reveals genetic bases of the flowering process in oriental hybrid lily cv. Sorbonne

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Abstract

Flowering is a critical step in plant reproduction. Oriental lily (Lilium) characterized by showy flowers is increasingly used; however, the blossom period is an important limiting factor influencing the value of lily. Improving the flowering of lily by molecular breeding technology has limitless applications, but the mechanism of the regulation of lily flowering remains to be studied. Transcriptomes providing comprehensive sequence profiling data of transcription variation during flowering process in Oriental hybrids lily Sorbonne were assembled from RNA-Seq data. Approximately 124.16 million 90 bp paired-end clean reads were assembled into 66 327 unigenes and compared with the UniProt databases. There are 30 254 unigenes that have significant hits to the sequences in the UniProt database, 60 738, 16 601, and 12 494 unigenes have similarity to the GO, KEGG, and COG databases, respectively. By analyzing dynamic changes in the transcriptome of lily flowering based on our RNA sequencing (RNA-Seq) data, some genes involved in floral induction were found, which revealed the complicated flower regulation network at the transcriptome level during lily flowering. Moreover, 12 DEGs related to flowering including LoLFY, LoMAF, LoFT, LoAG, LoCBF, LoAGL6a, LoSOC1, LoSEP1, LoNAC1, LoAPX, LoARF10, and LoICE were identified with real-time quantitative RT-PCR analysis. The results suggested that the flower of Oriental lily possessed a high proportion of flowering genes active at different stages of flowering. According to the results of the present study, we predicted that they would play an important role during flowering process; these data provided the foundation for future studies of metabolism during flowering of Oriental lily.

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Abbreviations

BLAST:

basic local alignment search tool

COG:

cluster of orthologous group

DEG:

differentially expressed genes

EST:

expressed sequence tag

GO:

gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

NCBI:

National Center for Biotechnology Information

NGS:

Next Generation Sequencing

qRT-PCR:

real-time quantitative reverse transcription polymerase chain reaction

RPKM:

reads per kilobases per million reads

References

  1. Lee, I.L., Kyong, C.P., Ye, S.S., Jae, H.S., Soon, J.K., Jong, K.N., Jong, H.K., and Nam, S.K., Development of expressed sequence tag derived-simple sequence repeats in the genus Lilium, Genes Genomics, 2011, vol. 33, pp. 727–733.

    Article  CAS  Google Scholar 

  2. Simpson, G.G. and Dean, C., Arabidopsis, the Rosetta stone of flowering time? Science, 2002, vol. 296, pp. 285–289.

    Article  PubMed  CAS  Google Scholar 

  3. Kuraparthy, V., Sood, S., and Gill, B.S., Genomic targeting and mapping of tiller inhibition gene (tin3) of wheat using ESTs and synteny with rice, Funct. Integr. Genomics, 2008, vol. 8, pp. 33–42.

    Article  PubMed  CAS  Google Scholar 

  4. Tzeng, T.Y. and Yang, C.H., A MADS-box gene from lily (Lilium longiflorum) is sufficient to generate dominant negative mutation by interacting with PISTIL-LATA (PI) in Arabidopsis thaliana, Plant Cell Physiol., 2001, vol. 42, pp. 1156–1168.

    Article  PubMed  CAS  Google Scholar 

  5. Tzeng, T.Y., Chen, H.Y., and Yang, C.H., Ectopic expression of carpel-specific MADS-box genes from lily and lisianthus causes similar homeotic conversion of sepal and petal in Arabidopsis, Plant Physiol., 2002, vol. 130, pp. 1827–1836.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  6. Tzeng, T.Y., Hsiao, C.C., and Chi, P.J., Two lily SEPALLATA-like genes cause different effects on floal formation and floral transition in Arabidopsis, Plant Physiol., 2003, vol. 133, pp. 1091–1101.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  7. Winter, K.U., Weister, C., Kerstin, K., Arend, B., Charlotte, K., Akira, K., Heinz, S., and Günter, T., Evolution of class B floral homeotic proteins: obligate heterodimerization originated from homodimerization, Mol. Biol. Evol., 2002, vol. 19, pp. 587–596.

    Article  PubMed  CAS  Google Scholar 

  8. Ness, R.W., Siol, M., and Barrett, S.C., De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants, BMC Genomics, 2011, vol. 12, p. 298.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  9. Yang, S.S., Tu, Z.J., Cheng, F., Xu, W.W., Lamb, J.F., Jung, H.J.G., Vance, C.P., and Gronwald, J.W., Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems, BMC Genomics, 2011, vol. 12, p. 199.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  10. Shi, C.Y., Yang, H., Wei, C.L., Yu, O., Zhang, Z.Z., Jiang, C.J., Sun, J., Li, Y.Y., Chen, Q., Xia, T., and Wan, X.C., Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds, BMC Genomics, 2011, vol. 12, p. 131.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  11. Li, R.Q., Zhu, H.M., Ruan, J., Qian, W.B., Fang, X.D., Shi, Z.B., Li, Y.R., Li, S.T., Shan, G., Kristiansen, K., Li, S.G., Yang, H.M., Wang, J., and Wang, J., De novo assembly of human genomes with massively parallel short read sequencing, Genome Res., 2010, vol. 20, pp. 265–272.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  12. Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M., and Robles, M., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 2005, vol. 21, pp. 3674–3676.

    Article  PubMed  CAS  Google Scholar 

  13. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M., KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res., 1999, vol. 27, pp. 29–34.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  14. Livak, K.J. and Schmittgen, T.D., Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCt method, Methods, 2001, vol. 25, pp. 402–408.

    Article  PubMed  CAS  Google Scholar 

  15. Okoniewski, M. and Miller, C., Hybridization interactions between probesels in short oligo microarrays lead to spurious correlations, BMC Bioinformatics, 2006, vol. 7, p. 276.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Qiu, Z.B. and Wan, L.C., The regulation of cambial activity in Chinese fir (Cunninghamia lanceolata) involves extensive transcriptome remodeling, New Phytol., 2013, vol. 199, pp. 708–719.

    Article  PubMed  CAS  Google Scholar 

  17. Scortecci, K.C., Michaels, S.D., and Amasino, R.M., Identification of a MADS-box gene, FLOWERING LOCUS M, that represses flowering, Plant J., 2001, vol. 26, pp. 229–236.

    Article  PubMed  CAS  Google Scholar 

  18. Helliwell, C.A., Wood, C.C., Robertson, M., Peacock, W.J., and Dennis, E.S., The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FTchromatin and is part of a high-molecular-weight protein complex, Plant J., 2006, vol. 46, pp. 183–192.

    Article  PubMed  CAS  Google Scholar 

  19. Johanson, U., West, J., Lister, C., Michaels, S., Amasino, R., and Dean, C., Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time, Science, 2000, vol. 290, pp. 344–347.

    Article  PubMed  CAS  Google Scholar 

  20. Schmitz, R.J. and Amasino, R.M., Vernalization: a model for investigating epigenetics and eukaryotic gene regulation in plants, Biochim. Biophys. Acta, 2007, vol. 1769, pp. 269–275.

    Article  PubMed  CAS  Google Scholar 

  21. Lee, J., Oh, M., Park, H., and Lee, I., SOC1 translocated to the nucleus by interaction with AGL24 directly regulates LEAFY, Plant J., 2008, vol. 55, pp. 832–843.

    Article  PubMed  CAS  Google Scholar 

  22. Zhong, X., Dai, X., Xv, J., Wu, H.Y., Liu, B., and Li, H.Y., Cloning and expression analysis of GmGAL1, SOC1 homolog gene in soybean, Mol. Biol. Rep., 2012, vol. 39, pp. 6967–6974.

    Article  PubMed  CAS  Google Scholar 

  23. Tan, F.C. and Swain, S.M., Functional characterization of AP3, SOC1 and WUS homologues from citrus (Citrus sinensis), Physiol. Plant., 2007, vol. 131, pp. 481–495.

    Article  PubMed  CAS  Google Scholar 

  24. Davletova, S., Rizhsky, L., Liang, H., Shengqiang, Z., Oliver, D.J., Coutu, J., Shulaev, V., Schlauch, K., and Mittler, R., Cytosolic ascorbate peroxidase 1 is a central component of the reactive oxygen gene network of Arabidopsis, Plant Cell, 2005, vol. 17, pp. 268–281.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  25. Srikanth, A. and Schmid, M., Regulation of flowering time: all roads lead to Rome, Cell. Mol. Life Sci., 2011, vol. 68, pp. 2013–2037.

    Article  PubMed  CAS  Google Scholar 

  26. Jung, C. and Muller, A.E., Flowering time control and applications in plant breeding, Trends Plant Sci., 2009, vol. 14, pp. 563–573.

    Article  PubMed  CAS  Google Scholar 

  27. Ietswaart, R., Wu, Z., and Dean, C., Flowering time control: another window to the connection between antisense RNA and chromatin, Trends Genetics, 2012, vol. 28, pp. 445–453.

    Article  CAS  Google Scholar 

  28. Seo, E., Lee, H., Jeon, J., Park, H., Kim, J., Noh, Y.S., and Lee, I., Crosstalk between cold response and flowering in Arabidopsis is mediated through the flowering-time gene SOC1 and its upstream negative regulator FLC, Plant Cell, 2009, vol. 21, pp. 3185–3197.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  29. Buzas, D.M., Robertson, M., Finnegan, E.J., and Helliwell, C.A., Transcription-dependence of histone H3 lysine 27 trimethylation at the Arabidopsis polycomb target gene FLC, Plant J., 2011, pp. 872–881.

    Google Scholar 

  30. Diallo, A., Kane, N., Agharbaoui, Z., Badawi, M., and Sarhan, F., Heterologous expression of wheat VERNALIZATION 2v (TaVRN2) gene in Arabidopsis delays flowering and enhances freezing tolerance, PLoS One, 2010, vol. 5: e8690.

    Article  PubMed  PubMed Central  Google Scholar 

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Author information

Authors and Affiliations

  1. College of Landscape Architecture, Beijing Forestry University, Beijing, P.R. China

    X. H. Liu, J. Huang, J. M. Wang & Y. M. Lu

  2. Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, P.R. China

    X. H. Liu, J. Huang, J. M. Wang & Y. M. Lu

  3. China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, P.R. China

    X. H. Liu, J. Huang, J. M. Wang & Y. M. Lu

Authors
  1. X. H. Liu
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  2. J. Huang
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  3. J. M. Wang
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  4. Y. M. Lu
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Correspondence to Y. M. Lu.

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This text was submitted by the authors in English.

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Liu, X.H., Huang, J., Wang, J.M. et al. RNA-Seq analysis reveals genetic bases of the flowering process in oriental hybrid lily cv. Sorbonne. Russ J Plant Physiol 61, 880–892 (2014). https://doi.org/10.1134/S1021443714060132

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  • DOI: https://doi.org/10.1134/S1021443714060132

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