Within and between whorls: Comparative transcriptional profiling of Aquilegia and Arabidopsis

PLoS ONE

Volumn 5, Issue 3, 2010, Pages

  Voelckel, Claudia ^a   Borevitz, Justin O ^b   Kramer, Elena M ^c   Hodges, Scott A ^d  

^a MASSEY UNIVERSITY   (New Zealand)

^b UNIVERSITY OF CHICAGO   (United States)

^c HARVARD UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PRIMER DNA;

AQUILEGIA; ARABIDOPSIS; ARTICLE; CELL CYCLE; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; FLOWER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; NUCLEIC ACID HYBRIDIZATION;

AQUILEGIA; ARABIDOPSIS; CELL CYCLE; DNA PRIMERS; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; FLOWERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 78651075760     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009735     Document Type: Article

References (49)

1. Ren D, Labandeira CC, Santiago-Blay JA, Rasnitsyn A, Shih C, et al. (2009) A probable pollination mode before angiosperms: Eurasian, long-proboscid scorpion flies. Science 326: 840-847.
2. Coen ES, Meyerowitz EM (1991) The war of the whorls-genetic interactions controlling flower development. Nature 353: 31-37.
3. Kalivas A, Pasentsis K, Polidoros AN, Tsaftaris AS (2007) Heterotopic expression of B-class floral homeotic genes PISTILLATA/GLOBOSA supports a modified model for crocus (Crocus sativus L.) flower formation. DNA Sequence 18: 120-130.
4. Kanno A, Saeki H, Kameya T, Saedler H, Theissen G (2003) Heterotopic expression of class B floral homeotic genes supports a modified ABC model for tulip (Tulipa gesneriana). Plant Molecular Biology 52: 831-841.
5. Kim S, Koh J, Yoo MJ, Kong HZ, Hu Y, et al. (2005) Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. Plant Journal 43: 724-744.
6. Bowman JL (1997) Evolutionary conservation of angiosperm flower development at the molecular and genetic levels. Journal of Biosciences 22: 515-527.
7. Irish VF (2009) Evolution of petal identity. Journal of Experimental Botany 60: 2517-2527.
8. Chanderbali AS, Albert VA, Leebens-Mack J, Altman NS, Soltis DE, et al. (2009) Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae). Proceedings of the National Academy of Sciences of the United States of America 106: 8929-8934.
9. Peiffer JA, Kaushik S, Sakai H, Arteaga-Vazquez M, Sanchez-Leon N, et al. (2008) A spatial dissection of the Arabidopsis floral transcriptome by MPSS. BMC Plant Biology 8.
10. Wellmer F, Riechmann JL, Alves-Ferreira M, Meyerowitz EM (2004) Genomewide analysis of spatial gene expression in Arabidopsis flowers. Plant Cell 16: 1314-1326.
11. Laitinen RAE, Immanen J, Auvinen P, Rudd S, Alatalo E, et al. (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.
12. Laitinen RAE, Pollanen E, Teeri TH, Elomaa P, Kotilainen M (2007) Transcriptional analysis of petal organogenesis in Gerbera hybrida. Planta 226: 347-360.
13. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34: 267-273.
14. Moore MJ, Bell CD, Soltis PS, Soltis DE (2007) Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proceedings of the National Academy of Sciences of the United States of America 104: 19363-19368.
15. Whittall JB, Hodges SA (2007) Pollinator shifts drive increasingly long nectar spurs in columbine flowers. Nature 447: 706-U712.
16. Hodges SA, Derieg NJ (2009) Adaptive radiations: From field to genomic studies. Proceedings of the National Academy of Sciences of the United States of America 106: 9947-9954.
17. Tucker SC, Hodges SA (2005) Floral ontogeny of Aquilegia, Semiaquilegia, and Enemion (Ranunculaceae). International Journal of Plant Sciences 166: 557-574.
18. Wang W, Chen ZD (2007) Generic level phylogeny of Thalictroideae (Ranunculaceae)-implications for the taxonomic status of Paropyrum and petal evolution. Taxon 56: 811-821.
19. Kramer EM, Holappa L, Gould B, Jaramillo MA, Setnikov D, et al. (2007) Elaboration of B gene function to include the identity of novel floral organs in the lower eudicot Aquilegia. Plant Cell 19: 750-766.
20. Kramer EM, Hodges SA (2010) Aquilegia as a model system for the evolution and ecology of petals. Philosophical Transactions of the Royal Society B: Biological Sciences 365: 477-490.
21. Whittall JB, Voelckel C, Kliebenstein DJ, Hodges SA (2006) Convergence, constraint and the role of gene expression during adaptive radiation: floral anthocyanins in Aquilegia. Molecular Ecology 15: 4645-4657.
22. Smyth DR, Bowman JL, Meyerowitz EM (1990) Early flower development in Arabidopsis. Plant Cell 2: 755-767.
23. Kramer EM, Jaramillo MA, Di Stilio VS (2004) Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms. Genetics 166: 1011-1023.
24. Soltis DE, Chanderbali AS, Kim S, Buzgo M, Soltis PS (2007) The ABC model and its applicability to basal angiosperms. Annals of Botany 100: 155-163.
25. Noda K, Glover BJ, Linstead P, Martin C (1994) Flower color intensity depends on specialized cell-shape controlled by a myb-related transcription factor. Nature 369: 661-664.
26. Erbar C, Kusma S, Leins P (1999) Development and interpretation of nectary organs in Ranunculaceae. Flora 194: 317-332.
27. Ronse De Craene LP (2007) Are petals sterile stamens or bracts? The origin and evolution of petals in the core eudicots. Ann Bot 100: 621-630.
28. Takhtajan (1991) Evolutionary trends in flowering plants. New York: Columbia University Press.
29. Baum DA (1998) The evolution of plant development. Current Opinion in Plant Biology 1: 79-86.
30. Kramer EM, Jaramillo MA (2005) Genetic basis for innovations in floral organ identity. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 304B: 526-535.
31. Bao X, Franks RG, Levin JZ, Liu Z (2004) Repression of AGAMOUS by BELLRINGER in floral and inflorescence meristems. Plant Cell 16: 1478-1489.
32. Yu LF, Patibanda V, Smith HMS (2009) A novel role of bell1-like homeobox genes, pennywise and pound-foolish, in floral patterning. Planta 229: 693-707.
33. Brambilla V, Battaglia R, Colombo M, Masiero S, Bencivenga S, et al. (2007) Genetic and molecular interactions between BELL1 and MADS box factors support ovule development in Arabidopsis. Plant Cell 19: 2544-2556.
34. Gould B, Kramer EM (2007) Virus-induced gene silencing as a tool for functional analyses in the emerging model plant Aquilegia (columbine, Ranunculaceae). Plant Methods 3.
35. Kramer EM (2009) Aquilegia: a new model for plant development, ecology, and evolution. Annual Review of Plant Biology 60: 261-277.
36. Bhuiyan NH, Selvaraj G, Wei YD, King J (2009) Gene expression profiling and silencing reveal that monolignol biosynthesis plays a critical role in penetration defence in wheat against powdery mildew invasion. Journal of Experimental Botany 60: 509-521.
37. Bindschedler LV, Dewdney J, Blee KA, Stone JM, Asai T, et al. (2006) Peroxidase-dependent apoplastic oxidative burst in Arabidopsis required for pathogen resistance. Plant Journal 47: 851-863.
38. Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, et al. (2006) Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant Cell and Environment 29: 1545-1570.
39. Torres MA, Dangl JL (2005) Functions of the respiratory burst oxidase in biotic interactions, abiotic stress and development. Current Opinion in Plant Biology 8: 397-403.
40. Weech MH, Chapleau M, Pan L, Ide C, Bede JC (2008) Caterpillar saliva interferes with induced Arabidopsis thaliana defence responses via the systemic acquired resistance pathway. Journal of Experimental Botany 59: 2437-2448.
41. Zabala G, Zou JJ, Tuteja J, Gonzalez DO, Clough SJ, et al. (2006) Transcriptome changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection. BMC Plant Biology 6.
42. Cooper EA, Whittall JB, Hodges SA, Nordborg M (2010) Genetic variation at nuclear loci fail to distinguish two morphologically distinct specis of Aquilegia. PLoS ONE 5(1): e8655. doi:10.1371/journal.pone.0008655.
43. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics 37: 501-506.
44. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, et al. (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Research 13: 513-523.
45. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
46. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the United States of America 98: 5116-5121.
47. Zhang X, Shiu S, Cal A, Borevitz JO (2008) Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. Plos Genetics 4.
48. Kim SY, Volsky DJ (2005) PAGE: Parametric analysis of gene set enrichment. BMC Bioinformatics 6.
49. Moreno-Hagelsieb G, Latimer K (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24: 319-324.