EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot

Plant Molecular Biology

Volumn 62, Issue 3, 2006, Pages 351-369

  Carlson, John E ^a   Leebens Mack, James H ^a,f   Wall, P Kerr ^a   Zahn, Laura M ^a,g   Mueller, Lukas A ^b   Landherr, Lena L ^a   Hu, Yi ^a   Ilut, Daniel C ^b   Arrington, Jennifer M ^a,c   Choirean, Stephanie ^a   Becker, Annette ^d   Field, Dawn ^e   Tanksley, Steven D ^b   Ma, Hong ^a   DePamphilis, Claude W ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c RANDOLPH COLLEGE   (United States)

^d UNIVERSITY OF BREMEN   (Germany)

^e CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

^f UNIVERSITY OF GEORGIA   (United States)

^g Science   (United States)

Author keywords

Basal eudicot; California poppy; EST database; Flower development

Indexed keywords

CALIFORNIA POPPY; EXPRESSED SEQUENCE TAGS; FLOWER DEVELOPMENT; SECONDARY METABOLISM;

DNA; GENES; METABOLISM; PLANTS (BOTANY);

MOLECULAR BIOLOGY;

COMPLEMENTARY DNA; MESSENGER RNA;

ARTICLE; EXPRESSED SEQUENCE TAG; FLOWER; GENE; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; IN SITU HYBRIDIZATION; PAPAVERACEAE; PHYLOGENY; PLANT GENE;

DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; FLOWERS; GENE EXPRESSION PROFILING; GENES, PLANT; IN SITU HYBRIDIZATION; PAPAVERACEAE; PHYLOGENY; RNA, MESSENGER;

FLOWERS; GENES; METABOLISM; NUCLEIC ACIDS; PLANTS;

ARABIDOPSIS; ESCHSCHOLZIA; ESCHSCHOLZIA CALIFORNICA; MAGNOLIOPHYTA; PAPAVER; PAPAVERACEAE;

EID: 33749033318     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-006-9025-y     Document Type: Article

References (71)

1. Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo M-J, Frohlich MW, Perl-Treves R, Schlarbaum S, Bliss B, Tanksley S, Oppenheimer DG, Soltis PS, Ma H, dePamphilis CW, Leebens-Mack JH (2005) Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol 5:5
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
3. Angenent GC, Franken J, Busscher M, Colombo L, van Tunen AJ (1993) Petal and stamen formation in petunia is regulated by the homeotic gene fpg1. Plant J 4:101-112
4. Angenent GC, Franken J, Busscher M, Weiss D, van Tunen AJ (1994) Co-suppression of the petunia homeotic gene fbp2 affects the identity of the generative meristem. Plant J 5:33-44
5. Becker A, Saedler H, Theissen G (2003) Distinct MADS-box gene expression patterns in the reproductive cones of the gymnosperm Gnetum gnemon. Dev Genes Evol 213:567-572
6. Becker S, Gleissbergy S, Smyth DR (2005) Floral and vegetative morphogenesis in California poppy (Eschscholzia californica Cham.). Int J Plant Sci 166:537-555
7. Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Phil Trans Royal Soc London B 274:227-274
8. Bennett MD, Bhandol P, Leitch IJ (2000) Nuclear DNA amounts in angiosperms and their modern uses - 807 new estimates. Annals Bot 86:859-909
9. Bennetzen JL, Coleman C, Liu R, Ma J, Ramakrishna W (2004) Consistent over-estimation of gene number in complex plant genomes. Curr Opion Plant Biol 7:732-736
10. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678
11. Bradley D, Carpenter R, Sommer H, Hartley N, Coen E (1993) Complementary floral homeotic phenotypes result from opposite orientations of a transposon at the PLENA locus of Antirrhinum. Cell 72:85-95
12. Busch A, Gleissberg S (2003) EcFLO, a FLORICAULA-like gene from Eschscholzia californica is expressed during organogenesis at the vegetative shoot apex. Planta 217:841-848
13. Castillo-Davis CI. (2005) The evolution of noncoding DNA: how much junk, how much func? Trends Genet 21:533-536
14. Clark C (1993) Papaveraceae (poppy family). In: Hickman JC (ed) The jepson manual, University of California Press, Berkeley, CA
15. Coen ES, Meyerowitz EM (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353:31-37
16. Coen ES, Romero JM, Doyle S, Elliott R, Murphy G, Carpenter R (1990) Floricaula - a homeotic gene required for flower development in Antirrhinum majus. Cell 63:1311-1322
17. Cook SA (1962) Genetic system, variation, and adaptation in Eschscholzia californica. Evolution 16:278-299
18. Decker G, Wanner G, Zenk MH, Lottspeich F (2000) Characterization of proteins in latex of the opium poppy (Papaver somniferum) using two-dimensional gel electrophoresis and microsequencing. Electrophoresis 21:3500-3516
19. Ditta G, Pinyopich A, Robles P, Pelaz S, Yanofsky MF (2004) The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Curr Biol 14:1935-1940
20. Endress PK (2004) Structure and relationships of basal relictual angiosperms. Aus Syst Bot 17:343-366
21. Flanagan CA, Ma H (1994) Spatially and temporally regulated expression of the MADs-Box gene AGL2 in wild-type and mutant Arabidopsis flowers. Plant Mol Biol 26:581-595
22. Frick S, Kramell R, Schmidt J, Fist AJ, Kutchan TM (2005) Comparative qualitative and quantitative determination of alkaloids in narcotic and condiment Papaver somniferum cultivars. J Nat Prod 68:666-673
23. Goldberg RB, Beals TP, Sanders PM (1993) Anther development: basic principles and practical applications. Plant Cell 5:1217-1229
24. Goto K, Meyerowitz EM (1994) Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes Dev 8:1548-1560
25. Groot EP, Sinha N, Gleissberg S (2005) Expression patterns of STM-like KNOX and Histone H4 genes in shoot development of the dissected-leaved basal eudicot plants Chelidonium majus and Eschscholzia californica (Papaveraceae). Plant Mol Biol 58:317-331
26. Huang H, Tudor M, Weiss CA, Hu Y, Ma H (1995) The Arabidopsis MADs-Box gene AGL3 is widely expressed and encodes a sequence-specific DNA-binding protein. Plant Mol Biol 28:549-567
27. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1999:138-148
28. Kramer EM, Irish VF (1999) Evolution of genetic mechanisms controlling petal development. Nature 399:144-148
29. Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17:1483-1498.
30. Kutchan TM (1995) Alkaloid biosynthesis-the basis for metabolic engineering of medicinal plants. Plant Cell 7:1059-1070
31. Lee J, Pedersen H (2001) Stable genetic transformation of Eschscholzia californica expressing synthetic green fluorescent proteins. Biotechnol Prog 17:247-251
32. Lincoln C, Long J, Meyerowitz E (2002) http//www.its.caltech. edu/~plantlab/protocols/insitu.htm, accessed August 27, 2004
33. Ma H (1994) The unfolding drama of flower development: recent results from genetic and molecular analyses. Genes Dev 8:745-756
34. Ma H (2005) Molecular genetic analyses of microsporogenesis and microgametogenesis in flowering plants. Annu Rev Plant Biol 56:393-434
35. Ma H (2006) A molecular portrait of Arabidopsis meiosis. In: The Arabidopsis Book. Somerville CR, Meyerowitz EM, Dangl J, Stitt M (eds), American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0009, http://www.aspb.org/ publications/arabidopsis/
36. Ma H, dePamphilis C (2000) The ABCs of floral evolution. Cell 101:5-8
37. McInerney JO (1998) GCUA: general codon usage analysis. Bioinformatics 14:372-373
38. Mandel MA, Yanofsky MF (1998) The Arabidopsis AGL9 MADS box gene is expressed in young flower primordial. Sex Plant Reprod 11:22-28
39. Memelink J (2004) Putting the opium in poppy to sleep. Nature Biotech 22:1526-1527
40. Nakamura Y, Gojobori T, Ikemura T (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res 28:292
41. Nanda KK, Sharma R (1976) Effects of gibberellic acid and cyclic 39,59-adenosine monophosphate on the flowering of Eschscholtzia californica Cham, a qualitative long day plant. Plant Cell Physiol 17:1093-1095
42. Park S-U, Facchini PJ (2000a) Agrobacterium rhizogenes-mediated transformation of opium poppy, Papaver somniferum L., and California poppy, Eschscholzia californica Cham., root cultures. J Exp Bot 51:1005-1016
43. Park S-U, Facchini PJ (2000b) Agrobacterium-mediated genetic transformation of California poppy, Eschscholzia californica Cham., via somatic embryogenesis. Plant Cell Rep 19:1006-1012
44. Park S-U, Min, Yu M, Facchini PJ (2002) Antisense RNA-mediated suppression of benzophenanthridine alkaloid biosynthesis in transgenic cell cultures of California poppy. Plant Physiol 128:696-706
45. Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF (2000) B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature 405:200-203
46. Sato F (2005) RNAi and functional genomics. Plant Biotech 22:431-442
47. Sato F, Hashimoto T, Hachiya A, Tamura K, Choi K-B, Morishige T, Fujimoto H, Yamada Y (2001) Metabolic engineering of plant alkaloid biosynthesis. Proc Natl Acad Sci USA 98:367-372
48. Savidge B, Rounsley SD, Yanofsky MF (1995) Temporal relationship between the transcription of two Arabidopsis MADS box genes and the floral organ identity genes. Plant Cell 7:721-733
49. Schneider H, Schuettpelz E, Pryer KM, Cranfill R, Magallon S, Lupia R (2004) Ferns diversified in the shadow of angiosperms. Nature 428:553-557
50. Schwarz-Sommer Z, Huijser P, Nacken W, Saedler H, Sommer H (1990) Genetic control of flower development in Antirrhinum majus. Science 250:931-936
51. Simon R, Carpenter R, Doyle S, Coen E (1994) Fimbriata controls flower development by mediating between meristem and organ identity genes. Cell 78:99-107
52. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195-197
53. Smyth DR, Bowman JL, Meyerowitz EM (1990) Early flower development in Arabidopsis. Plant Cell 2:755-767
54. Soltis D, Soltis P, Albert V, Oppenheimer D, Frohlich MW, dePamphilis CW, Ma H, Theissen G (2002) Missing links: the genetic architecture of flower and floral diversification. Trends Plant Sci 7:22-31
55. Soltis PS, Soltis DE, Kim S, Chanderbali A, Buzgo M (2006) Modifications of the ABC model based on analyses of basal angiosperms. In: Soltis DE, Soltis PS, Leebens-Mack JH (eds) Developmental genetics of the flower. Advances in botanical research series. Elsevier Limited, London. In press
56. Soltis PS, Soltis DE, Zanis MJ, Kim S (2000) Basal lineages of angiosperms: Relationships and implications for floral evolution. Int J Plant Sci 161:S97-S107
57. Sommer H, Beltran J-P, Huijser P, Pape H, Lonnig W-E, Saedler H, Schwarz-Sommer Z (1990) Deficiens, a homeotic gene involved in the control of flower morphogenesis in Antirrhinum majus: the protein shows homology to transcription factors. EMBO J 9:605-613
58. Thomas SG, Franklin-Tong VE (2004) Self-incompatibility triggers programmed cell death in Papaver pollen. Nature 429:305-309
59. Trémousaygue D, Garnier L, Bardet C, Dabos P, Hervécure B (2003) Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant J 33:957-966
60. Tremousaygue D, Manevski A, Bardet C, Lescure N, Lescure B (1999) Plant interstitial telomere motifs participate in the control of gene expression in root meristems. Plant J 20:553-562
61. Tröbner W, Ramirez L, Motte P, Hue I, Huijser P, Lönnig W-E, Saedler H, Sommer H, Schwarz-Sommer Z (1992) GLOBOSA: a homeotic gene which interacts with DEFICIENS in the control of Antirrhinum floral organogenesis. EMBO J 11:4693-4704
62. Wakelin AM, Lister CE, Conner AJ (2003) Inheritance and biochemistry of pollen pigmentation in California poppy (Eschscholzia californica Cham.). Int J Plant Sci 164:867-875
63. Weigel D, Meyerowitz EM (1994) The ABCs of floral homeotic genes. Cell 78:203-209
64. Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz EM (1992) LEAFY controls floral meristem identity in Arabidopsis. Cell 69:843-859
65. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
66. Yanofsky MF, Ma H, Bowman JL, Drews GN, Feldmann KA, Meyerowitz EM (1990) The protein encoded by the Arabidopsis homeotic gene AGAMOUS resembles transcription factors. Nature 346:35-43
67. Zahn LM, Kong H, Leebens-Mack JH, Kim S, Soltis PS, Landherr LL, Soltis DE, dePamphilis CW, Ma H (2005a) The evolution of the SEPALLATA subfamily of MADS-box genes: a pre-angiosperm origin with multiple duplications throughout angiosperm history. Genetics 169:2209-2223
68. Zahn LM, Leebens-Mack J, Arrington JM, Hu Y, Landherr L, dePamphilis CW, Becker A, Theissen G, Ma H (2006) Conservation and divergence in the AGAMOUS subfamily of MADS-Box genes: evidence of independent sub- and neofunctionalization events. Evol Dev 8:30-45
69. Zahn LM, Leebens-Mack J, DePamphilis CW, Ma H, Theissen G (2005b) To B or not to B a flower: The role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. J Hered 96:225-240
70. Zhang X, Feng B, Zhang Q, Zhang D, Altman N, Ma H (2005) Genome-wide expression profiling and identification of gene activities during early flower development in Arabidopsis. Plant Mol Biol 58:401-419
71. Zhao D, Yu Q, Chen C, Ma H (2001) Genetic control of reproductive meristems. In: McManus MT, Veit B (eds) Meristematic tissues in plant growth and development. Academic Press, Sheffield, pp 89-142