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Articles

Transcriptome and flower genes analysis of Prunus campanulata Maxim

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Pages 44-52 | Accepted 01 Jul 2019, Published online: 22 Jul 2019

References

  • Abe, M., Kobayashi, Y., Yamamoto, S., Daimon, Y., Yamaguchi, A., Ikeda, Y., … Araki, T. (2005). FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science, 309, 1052–1056. doi:10.1126/science.1115983
  • Ahn, J.H., Miller, D., Winter, V.J., Banfield, M.J., Jeong, H.L., So, Y.Y., … Weigel, D. (2006). A divergent external loop confers antagonistic activity on floral regulators FT and TFL1. EMBO Journal, 25, 605–614. doi:10.1038/sj.emboj.7600950
  • Amasino, R. (2010). Seasonal and developmental timing of flowering. The Plant Journal, 61, 1001–1013. doi:10.1111/j.1365-313X.2010.04148.x
  • Babenko, V.N., Rogozin, I.B., Mekhedov, S.L., & Koonin, E.V. (2004). Prevalence of intron gain over intron los in the evolution of paralogous gene families. Nucleic Acids Research, 32, 3724–3733. doi:10.1093/nar/gkh686
  • Bendahmane, M., Dubois, A., Raymond, O., & Bris, M.L. (2013). Genetics and genomics of flower initiation and development in roses. Journal of Experimental Botany, 64, 847–857. doi:10.1093/jxb/ers387
  • Bielenberg, D.G., Wang, Y., Li, Z., Zhebentyayeva, T., Fan, S., Reighard, G.L., … Abbott, A.G. (2008). Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation. Tree Genetics and Genomes, 4, 495–507. doi:10.1007/s11295-007-0126-9
  • Blázquez, M.A. (2000). Flower development pathways. Journal of Cell Science, 113, 3547–3548.
  • Böhlenius, H., Huang, T., Charbonnel-Campaa, L., Brunner, A.M., Jansson, S., Strauss, S.H., & Nilsson, O. (2006). CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science, 312, 1040–1044. doi:10.1126/science.1126038
  • Bowman, J.L., Smyth, D.R., & Meyerowitz, E.M. (1989). Genes directing flower development in Arabidopsis. The Plant Cell, 1, 37–52. doi:10.1105/tpc.1.1.37
  • Cai, S., & Lashbrook, C.C. (2008). Stamen abscission zone transcriptome profiling reveals new candidates for abscission control : Enhanced retention of floral organs in transgenic plants overexpressing Arabidopsis ZINC FINGER PROTEIN2. Plant Physiology, 146, 1305–1321. doi:10.1104/pp.107.110908
  • Castède, S., Campoy, J.A., García, J.Q., LeDantec, L., Lafargue, M., Barreneche, T., … Dirlewanger, E. (2014). Genetic determinism of phenological traits highly affected by climate change in Prunus avium: Flowering date dissected into chilling and heat requirements. New Phytologist, 202, 703–715. doi:10.1111/nph.12658
  • Chardon, F., & Damerval, C. (2005). Phylogenomic analysis of the PEBP gene family in cereals. Journal of Molecular Evolution, 61, 579–590. doi:10.1007/s00239-004-0179-4
  • Chen, S.Y., Chien, C.Te, Chung, J.Der, Yang, Y.S., & Kuo, S.R. (2007). Dormancy-break and germination in seeds of Prunus campanulata (Rosaceae): Role of covering layers and changes in concentration of abscisic acid and gibberellins. Seed Science Research, 17, 21–32. doi:10.1017/S0960258507383190
  • Cheng, Y., Dai, X., & Zhao, Y. (2007). Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis. The Plant Cell, 19, 2430–2439. doi:10.1105/tpc.107.053009
  • Chien, C., Chen, S., & Yang, J.-C. (2002). Effect of stratification and drying on the germination and storage of Prunus campanulata seeds. Taiwan Journal of Forest Science, 17, 413–420.
  • Clouse, S.D. (2011). Brassinosteroid signal transduction: From receptor kinase activation to transcriptional networks regulating plant development. The Plant Cell, 23, 1219–1230. doi:10.1105/tpc.111.084475
  • Cockram, J., Jones, H., Leigh, F.J., Sullivan, D.O., Powell, W., Laurie, D.A., & Greenland, A.J. (2007). Control of flowering time in temperate cereals: Genes, domestication, and sustainable productivity. Journal of Experimental Botany, 58, 1231–1244. doi:10.1093/jxb/erm042
  • Coen, E.S., & Meyerowitz, E.M. (1991). The war of the whorls: Genetic interactions controlling flower development. Nature, 353, 31–37. doi:10.1038/353031a0
  • Collaudin, S. (2013). Morphogenesis of the flower of Arabidopsis, genes networks and mathematical modelling. BioSciences Master Reviews, 1–10.
  • Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I., … Coupland, G. (2007). FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science, 316, 1030–1033. doi:10.1126/science.1141752
  • Doi, H. (2007). Winter flowering phenology of Japanese apricot Prunus mume reflects climate change across Japan. Climate Research, 34, 99–104. doi:10.3354/cr034099
  • Egan, A.N., Schlueter, J., & Spooner, D.M. (2012). Applications of next-generation sequencing in plant biology. American Journal of Botany, 99, 175–185. doi:10.3732/ajb.1200020
  • Fiers, W., Contreas, R., Duerinck, F., Haegeman, G., Iserentant, D., Merregaert, J., … Ysebaert, M. (1976). Complete nucleotide sequence of bacteriophage MS2 RNA: Primary and secondary structure of the replicase gene. Nature, 260, 500–507. doi:10.1038/260500a0
  • Franco-Zorrilla, J.M., López-Vidriero, I., Carrasco, J.L., Godoy, M., Vera, P., & Solano, R. (2014). DNA-binding specificities of plant transcription factors and their potential to define target genes. Proceedings of the National Academy of Sciences, 111, 2367–2372. doi:10.1073/pnas.1316278111
  • Frugoli, J.A., McPeek, M.A., Thomas, T.L., & Robertson McClung, C. (1998). Intron loss and gain during evolution of the catalase gene family in angiosperms. Genetics, 149, 355–365. doi:10.1002/9780470015902.a0020785
  • Galla, G., Vogel, H., Sharbel, T.F., & Barcaccia, G. (2015). De novo sequencing of the Hypericum perforatum L. flower transcriptome to identify potential genes that are related to plant reproduction sensu lato. BMC Genomics, 16, 1–22. doi:10.1186/s12864-015-1439-y
  • Guo, L., Dai, J., Wang, M., Xu, J., & Luedeling, E. (2015). Responses of spring phenology in temperate zone trees to climate warming: A case study of apricot flowering in China. Agricultural and Forest Meteorology, 201, 1–7. doi:10.1016/j.agrformet.2014.10.016
  • Hanzawa, Y., Money, T., & Bradley, D. (2005). A single amino acid converts a repressor to an activator of flowering. Proceedings of the National Academy of Sciences, 102, 7748–7753. doi:10.1073/pnas.0500932102
  • Harig, L., Beinecke, F.A., Oltmanns, J., Muth, J., Müller, O., Rüping, B., … Noll, G.A. (2012). Proteins from the FLOWERING LOCUS T-like subclade of the PEBP family act antagonistically to regulate floral initiation in tobacco. The Plant Journal, 72, 908–921. doi:10.1111/j.1365-313X.2012.05125.x
  • Hou, J.H., Gao, Z.H., Zhang, Z., Chen, S.M., Ando, T., Zhang, J.Y., & Wang, X.W. (2011). Isolation and characterization of an AGAMOUS Homologue PmAG from the Japanese Apricot (Prunus mume Sieb. et Zucc.). Plant Molecular Biology Reporter, 29, 473–480. doi:10.1007/s11105-010-0248-3
  • Huang, J.Z., Lin, C.P., Cheng, T.C., Chang, B.C.H., Cheng, S.Y., Chen, Y.W., … Chen, F.C. (2015). A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development. PloS One, 10, 1–20. doi:10.1371/journal.pone.0123474
  • Karlgren, A., Gyllenstrand, N., Kallman, T., Sundstrom, J.F., Moore, D., Lascoux, M., & Lagercrantz, U. (2011). Evolution of the PEBP gene family in plants: Functional diversification in seed plant evolution. Plant Physiology, 156, 1967–1977. doi:10.1104/pp.111.176206
  • Kim, S.Y., Zhu, T., & Sung, Z.R. (2010). Epigenetic regulation of gene programs by EMF1 and EMF2 in Arabidopsis. Plant Physiology, 152, 516–528. doi:10.1104/pp.109.143495
  • Laitinen, R.A.E., Immanen, J., Auvinen, P., Rudd, S., Alatalo, E., Paulin, L., … Elomaa, P. (2005). Analysis of the floral transcriptome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae). Genome Research, 15, 475–486. doi:10.1101/gr.3043705
  • Lee, C.S., Chien, C.T., Lin, C.H., Chiu, Y.Y., & Yang, Y.S. (2006). Protein changes between dormant and dormancybroken seeds of Prunus campanulata Maxim. Proteomics, 6, 4147–4154. doi:10.1002/pmic.200500118
  • Lee, X.W., Mat-Isa, M.N., Mohd-Elias, N.A., Aizat-Juhari, M.A., Goh, H.H., Dear, P.H., … Wan, K.L. (2016). Perigone lobe transcriptome analysis provides insights into rafflesia cantleyi flower development. PLoS One, 11, 1–18. doi:10.1371/journal.pone.0167958
  • Liu, C., Zhang, J., Zhang, N., Shan, H., Su, K., Zhang, J., … Chen, Z. (2010). Interactions among proteins of floral MADS-box genes in basal eudicots: Implications for evolution of the regulatory network for flower development. Molecular Biology and Evolution, 27, 1598–1611. doi:10.1093/molbev/msq044
  • Liu, L.-Y.D., Tseng, H.-I., Lin, C.-P., Lin, -Y.-Y., Huang, Y.-H., Huang, C.-K., … Lin, -S.-S. (2014). High-throughput transcriptome analysis of the leafy flower transition of Catharanthus roseus induced by peanut witches ’ -broom phytoplasma infection. Plant and Cell Physiology, 55, 942–957. doi:10.1093/pcp/pcu029
  • Liu, Z., Zhang, D., Liu, D., Li, F., & Lu, H. (2013). Exon skipping of AGAMOUS homolog PrseAG in developing double flowers of Prunus lannesiana (Rosaceae). Plant Cell Reports, 32, 227–237. doi:10.1007/s00299-012-1357-2
  • Lulin, H., Xiao, Y., Pei, S., Wen, T., & Shangqin, H. (2012). The first illumina-based De Novo transcriptome sequencing and analysis of safflower flowers. PloS One, 7, 1–11. doi:10.1371/journal.pone.0038653
  • Ma, K.-F., Zhang, Q.-X., Cheng, T.-R., Yan, X.-L., Pan, H.-T., & Wang, J. (2018). Substantial epigenetic variation causing flower color chimerism in the ornamental tree Prunus mume revealed by single base resolution methylome detection and transcriptome sequencing. International Journal of Molecular Sciences, 19, 2315. doi:10.3390/ijms19082315
  • Menzel, A., Sparks, T.H., Estrella, N., Koch, E., Aasa, A., Ahas, R., … Zust, A. (2006). European phenological response to climate change matches the warming pattern. Global Change Biology, 12, 1969–1976. doi:10.1111/j.1365-2486.2006.01193.x
  • Mitsuda, N., Seki, M., Shinozaki, K., & Ohme-takagi, M. (2005). The NAC transcription factors NST1 and NST2 of Arabidopsis regulate secondary wall thickenings and are required for anther Dehiscence. The Plant Cell, 17, 2993–3006. doi:10.1105/tpc.105.036004
  • Nordborg, M., & Weigel, D. (2008). Next-generation genetics in plants. Nature, 456, 720–723. doi:10.1038/nature07629
  • Ou, S.-K., & Chen, C.-L. (2002). Chilling requirement for native Prunus campanulata Maxim in Taiwan. Journal of Taiwan Agricultural Research, 51, 25–32.
  • Parcy, F. (2005). Flowering: A time for integration. The International Journal of Developmental Biology, 49, 585–593. doi:10.1387/ijdb.041930fp
  • Pareek, C.S., Smoczynski, R., & Tretyn, A. (2011). Sequencing technologies and genome sequencing. Journal of Applied Genetics, 52, 413–435. doi:10.1007/s13353-011-0057-x
  • Pařenicová, L., deFolter, S., Kieffer, M., Horner, D.S., Favalli, C., Busscher, J., … Colombo, L. (2003). Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: New openings to the MADS world. The Plant Cell, 15, 1538–1551. doi:10.1105/tpc.011544
  • Pavey, S.A., Bernatchez, L., Aubin-Horth, N., & Landry, C.R. (2012). What is needed for next-generation ecological and evolutionary genomics? Trends in Ecology and Evolution, 27, 673–676. doi:10.1016/j.tree.2012.07.014
  • Ramos, M.J.N., Coito, J.L., Fino, J., Cunha, J., Silva, H., deAlmeida, P.G., … Rocheta, M. (2017). Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification. Plant Molecular Biology, 93, 151–170. doi:10.1007/s11103-016-0553-9
  • Roy, S.W., & Gilbert, W. (2006). The evolution of spliceosomal introns: Patterns, puzzles and progress. Nature Reviews Genetics, 7, 211–221. doi:10.1038/nrg1807
  • Sanger, F., Nicklen, S., & Coulson, A.R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74, 5463–5467. doi:10.1073/pnas.74.12.5463
  • Schuster, S.C. (2008). Next-generation sequencing transforms today’s biology. Nature Methods, 5, 16–18. doi:10.1038/nmeth1156
  • Searle, I., He, Y., Turck, F., Vincent, C., Fornara, F., Kröber, S., … Coupland, G. (2006). The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes & Development, 20, 898–912. doi:10.1101/gad.373506
  • Sherman, W.B., & Lyrene, P.M. (2003). Low chill breeding of deciduous fruits at the University of Florida. Acta Horticulturae, 622, 599–605. doi:10.17660/ActaHortic.2003.622.65
  • Singh, V.K., Garg, R., & Jain, M. (2013). A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnology Journal, 11, 691–701. doi:10.1111/pbi.12059
  • Smyth, D.R., Bowman, J.L., & Meyerowitz, E.M. (1990). Early flower development in Arabidopsis. The Plant Cell, 2, 755–767.
  • Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596–1599. doi:10.1093/molbev/msm092
  • Tani, E., Polidoros, A.N., Flemetakis, E., Stedel, C., Kalloniati, C., Demetriou, K., … Tsaftaris, A.S. (2009). Plant physiology and biochemistry Characterization and expression analysis of AGAMOUS-like, SEEDSTICK-like, and SEPALLATA-like MADS-box genes in peach (Prunus persica) fruit. Plant Physiology Et Biochemistry, 47, 690–700. doi:10.1016/j.plaphy.2009.03.013
  • Teo, N.W.Z., Song, S., Wang, Y.-Q., Liu, J., & Yu, H. (2014). New insights into the regulation of inflorescence architecture. Trends in Plant Science, 19, 158–165. doi:10.1016/j.tplants.2013.11.001
  • Theißen, G. (2001). Development of floral organ identity: Stories from the MADS house. Current Opinion in Plant Biology, 4, 75–85. doi:10.1016/S1369-5266(00)00139-4
  • Ubi, B.E., Saito, T., Bai, S., Nishitani, C., Ban, Y., Ikeda, K., … Moriguchi, T. (2013). Characterization of 10 MADS-box genes from pyrus pyrifolia and their differential expression during fruit development and ripening. Gene, 528, 183–194. doi:10.1016/j.gene.2013.07.018
  • Weigel, D., Alvarez, J., Smyth, D.R., Yanofsky, M.F., & Meyerowitz, E.M. (1992). LEAFY controls floral meristem identity in arabidopsis. Cell, 69, 643–659. doi:10.1016/0092-8674(92)90295-N
  • Wen, C., Lin, S., & Chu, F. (2015). Transcriptome analysis of a subtropical deciduous tree : Autumn leaf senescence gene expression profile of formosan gum. Plant and Cell Physiology,56, 163–174. doi:10.1093/pcp/pcu160
  • Zhu, Y., Li, Y., Xin, D., Chen, W., Shao, X., Wang, Y., & Guo, W. (2015). RNA-Seq-based transcriptome analysis of dormant flower buds of Chinese cherry (Prunus pseudocerasus). Gene, 555, 362–376. doi:10.1016/j.gene.2014.11.032

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