Zhang et al. BMC Genomics 2011, 12:63 http://www.biomedcentral.com/1471-2164/12/63 25. Li ZM, Zhang JZ, Mei L, Deng XX, Hu CG, Yao JL: PtSVP, an SVP homolog from trifoliate orange (Poncirus trifoliata L. Raf.), shows seasonal periodicity of meristem determination and affects flower development in transgenic Arabidopsis and tobacco plants. Plant Mol Biol 2010, 74:129-142. 26. Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, Kirkness EF, Weinstock KG, Gocayne JD, White O: Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 1995, 377(6547 Suppl):371-374. 27. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. Science 1995, 270(5235):484-487. 28. Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild CD: Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotechnol 2004, 22(8):1006-1011. 29. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M: Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000, 18(6):630-634. 30. Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, Edberg SB, Ghazal H, Decola S: The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res 2004, 14(8):1641-1653. 31. Iandolino A, Nobuta K, Da Silva FG, Cook DR, Meyers BC: Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures. BMC Plant Biol 2008, 8(1):53. 32. Guo M, Yang S, Rupe M, Hu B, Bickel DR, Arthur L, Smith O: Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS(tm)) Reveals cis-and trans-effects on gene expression in maize hybrid meristem tissue. Plant Mol Biol 2008, 66(5):551-563. 33. Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, Edberg SB, Ghazal H, Decola S: The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res 2004, 14(8):1641. 34. Kal AJ, Van Zonneveld AJ, Benes V, Van Den Berg M, Koerkamp MG, Albermann K, Strack N, Ruijter JM, Richter A, Dujon B: Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol Biol Cell 1999, 10(6):1859-1872. 35. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M: Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 2003, 302(5646):842-846. 36. Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K: Sequencing and analysis of approximately 40 000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res 2008, 15(6):333-346. 37. Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA: Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 2006, 60(1):69-85. 38. Ralph SG, Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM: Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics 2008, 9(1):57. 39. Jia J, Fu J, Zheng J, Zhou X, Huai J, Wang J, Wang M, Zhang Y, Chen X, Zhang J: Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. Plant J 2006, 48(5):710-727. 40. Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu YP, Bouck J, Flavell RB: Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 2009, 69(1):179-194. 41. Iseli C, Jongeneel CV, Bucher P: ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. International Conference on Intelligent Systems for Molecular Biology: 1999 1999, 138-148. 42. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K: TRANSFAC (R) and its module TRANSCompel (R): transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34(Database Issue):D108. Page 19 of 20 43. Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J: PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res 2008, 36(Database issue):D966. 44. Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD: Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 2003, 31(19):5654. 45. He Y, Michaels SD, Amasino RM: Regulation of flowering time by histone acetylation in Arabidopsis. Science 2003, 302(5651):1751. 46. Pillitteri LJ, Lovatt CJ, Walling LL: Isolation and characterization of LEAFY and APETALA1 homologues from Citrus sinensis L. Osbeck’Washington’. J Am Soc Hort Sci 2004, 129:846-856. 47. Iandolino A, Nobuta K, Da Silva F, Cook D, Meyers B: Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures. BMC Plant Biol 2008, 8(1):53. 48. Xu Q, Yu K, Zhu A, Ye J, Liu Q, Zhang J, Deng X: Comparative transcripts profiling reveals new insight into molecular processes regulating lycopene accumulation in a sweet orange (Citrus sinensis) red-flesh mutant. BMC Genomics 2009, 10(1):540. 49. Hoth S, Morgante M, Sanchez JP, Hanafey MK, Tingey SV, Chua NH: Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant. J Cell Sci 2002, 115(24):4891-4900. 50. Fontanillas P, Landry CR, Wittkopp PJ, Russ C, Gruber JD, Nusbaum C, Hartl DL: Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol Ecol 2010, 19(s1):212-227. 51. Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, Harris RA, O’Hare MJ, Neville AM, Simpson AJG: Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci USA 2003, 100(8):4702-4705. 52. Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, Kuznetsov D, Stevenson BJ, Strausberg RL, Simpson AJG: An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res 2005, 15(7):1007-1014. 53. Meyers BC, Lee DK, Vu TH, Tej SS, Edberg SB, Matvienko M, Tindell LD: Arabidopsis MPSS. An online resource for quantitative expression analysis. Plant Physiol 2004, 135(2):801-813. 54. Hedgecock D, Lin JZ, DeCola S, Haudenschild CD, Meyer E, Manahan DT, Bowen B: Transcriptomic analysis of growth heterosis in larval Pacific oysters (Crassostrea gigas). Proc Natl Acad Sci 2007, 104(7):2313-2318. 55. Koshita Y, Takahara T, Ogata T, Goto A: Involvement of endogenous plant hormones (IAA, ABA, GAs) in leaves and flower bud formation of satsuma mandarin (Citrus unshiu Marc.). Scientia Horticulturae 1999, 79(3-4):185-194. 56. McArtney SJ: Exogenous gibberellin affects biennial bearing and the fruit shape of ‘Braeburn’ apple. New Zealand J Crop Hort Sci 1994, 22(3):343-346. 57. Inglese P, Chessa I, La Mantia T, Nieddu G: Evolution of endogenous gibberellins at different stages of flowering in relation to return bloom of cactus pear (Opuntia ficus-indica L. Miller). Scientia Horticulturae 1998, 73(1):45-51. 58. Anderson JL, Seeley SD: Bloom delay in deciduous fruits. Hort Rev 1993, 15:97-144. 59. Lee J, Lee I: Regulation and function of SOC1, a flowering pathway integrator. J Exp Bot 2010, 61(9):2247-2254. 60. Tan FC, Swain SM: Functional characterization of AP3, SOC1 and WUS homologues from citrus (Citrus sinensis). Physiologia Plantarum 2007, 131(3):481-495. 61. Cervera M, Navarro L, Pe aL: Gene stacking in 1-year-cycling APETALA1 citrus plants for a rapid evaluation of transgenic traits in reproductive tissues. J Biotechnol 2009, 140(3-4):278-282. 62. Valverde F, Mouradov A, Soppe W, Ravenscroft D, Samach A, Coupland G: Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 2004, 303(5660):1003. 63. Reeves PA, He Y, Schmitz RJ, Amasino RM, Panella LW, Richards CM: Evolutionary conservation of the FLOWERING LOCUS C-mediated