Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms

New Phytologist

Volumn 180, Issue 2, 2008, Pages 408-420

  Quesada, Tania ^a   Li, Zhen ^b   Dervinis, Christopher ^a   Li, Yao ^b   Bocock, Philip N ^a   Tuskan, Gerald A ^c,d   Casella, George ^a,b   Davis, John M ^a   Kirst, Matias ^a  

^a UNIVERSITY OF FLORIDA   (United States)

^b Oak Ridge National Laboratory ^*  (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Arabidopsis thaliana; Comparative genomics; Evolution; Populus trichocarpa; Transcriptome; Woody

Indexed keywords

CHROMOSOME; COMPARATIVE STUDY; DICOTYLEDON; DIVERGENCE; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOMICS; HOMOLOGY; RNA; SPECIES DIVERSITY;

ANGIOSPERM; ARABIDOPSIS; ARTICLE; ASPEN; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR EVOLUTION; PLANT; PLANT GENE; PLANT GENOME;

ANGIOSPERMS; ARABIDOPSIS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; PLANT COMPONENTS; POPULUS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; MAGNOLIOPHYTA; POPULUS TRICHOCARPA;

EID: 52649117161     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2008.02586.x     Document Type: Article

References (44)

1. Arava Y, Wang YL, Storey JD, Liu CL, Brown PO, Herschlag D. 2003. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences, USA 100 : 3889 3894.
2. Aspeborg H, Schrader J, Coutinho PM, Stam M, Kallas A, Djerbi S, Nilsson P, Denman S, Amini B, Sterky F et al. 2005. Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen. Plant Physiology 137 : 983 997.
3. Baltimore D. 2001. Our genome unveiled. Nature 409 : 814 816.
4. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate - a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B - Methodological 57 : 289 300.
5. Bitonti MB, Cozza R, Chiappetta A, Giannino D, Castiglione MR, Dewitte W, Mariotti D, Van Onckelen H, Innocenti AM. 2002. Distinct nuclear organization, DNA methylation pattern and cytokinin distribution mark juvenile, juvenile-like and adult vegetative apical meristems in peach (Prunus persica (L.) Batsch). Journal of Experimental Botany 53 : 1047 1054.
6. Bohlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Jansson S, Strauss SH, Nilsson O. 2006. CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312 : 1040 1043.
7. Bradshaw HD, Ceulemans R, Davis J, Stettler R. 2000. Emerging model systems in plant biology: poplar (Populus) as a model forest tree. Journal of Plant Growth Regulation 19 : 306 313.
8. Brunner AM, Busov VB, Strauss SH. 2004a. Poplar genome sequence: functional genomics in an ecologically dominant plant species. Trends in Plant Science 9 : 49 56.
9. Brunner AM, Yakovlev IA, Strauss SH. 2004b. Validating internal controls for quantitative plant gene expression studies. BMC Plant Biology 4 : 14.
10. Chang S, Puryear J, Cairney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 11 : 117 121.
11. Chu TM, Weir B, Wolfinger R. 2002. A systematic statistical linear modeling approach to oligonucleotide array experiments. Mathematical Biosciences 176 : 35 51.
12. Cohen BA, Mitra RD, Hughes JD, Church GM. 2000. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genetics 26 : 183 186.
13. Cooke JEK, Martin TA, Davis JM. 2005. Short-term physiological and developmental responses to nitrogen availability in hybrid poplar. New Phytologist 167 : 41 52.
14. Doebley J, Lukens L. 1998. Transcriptional regulators and the evolution of plant form. Plant Cell 10 : 1075 1082.
15. Fraga MF, Canal MJ, Rodriguez R. 2002a. In vitro morphogenic potential of differently aged Pinus radiata trees correlates with polyamines and DNA methylation levels. Plant Cell Tissue and Organ Culture 70 : 139 145.
16. Fraga MF, Rodriguez R, Canal MJ. 2002b. Genomic DNA methylation- demethylation during aging and reinvigoration of Pinus radiata. Tree Physiology 22 : 813 816.
17. Groover AT. 2005. What genes make a tree a tree? Trends in Plant Sciences 10 : 210 214.
18. Khaitovich P, Enard W, Lachmann M, Paabo S. 2006. Evolution of primate gene expression. Nature Reviews Genetics 7 : 693 702.
19. King MC, Wilson AC. 1975. Evolution at 2 levels in humans and chimpanzees. Science 188 : 107 116.
20. Kirst M, Johnson AF, Baucom C, Ulrich E, Hubbard K, Staggs R, Paule C, Retzel E, Whetten R, Sederoff R. 2003. Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA 100 : 7383 7388.
21. Levine M, Tjian R. 2003. Transcription regulation and animal diversity. Nature 424 : 147 151.
22. Ma L, Sun N, Liu X, Jiao Y, Zhao H, Deng XW. 2005. Organ-specific expression of Arabidopsis genome during development. Plant Physiology 138 : 80 91.
23. Ma LG, Chen C, Liu XG, Jiao YL, Su N, Li L, Wang XF, Cao ML, Sun N, Zhang XQ et al. 2005. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Research 15 : 1274 1283.
24. Mellerowicz EJ, Baucher M, Sundberg B, Boerjan W. 2001. Unravelling cell wall formation in the woody dicot stem. Plant Molecular Biology 47 : 239 274.
25. Moyle R, Schrader J, Stenberg A, Olsson O, Saxena S, Sandberg G, Bhalerao RP. 2002. Environmental and auxin regulation of wood formation involves members of the AUX/IAA gene family in hybrid aspen. Plant Journal 31 : 675 685.
26. Neill S. 2005. No way to die - nitric oxide, programmed cell death and xylogenesis. New Phytologist 165 : 5 7.
27. O'Brien KP, Remm M, Sonnhammer ELL. 2005. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Research 33 : D476 D480.
28. O'Brien PC, Dyck PJ. 1985. A runs test based on run lengths. Biometrics 41 : 237 244.
29. Paux E, Carocha V, Marques C, Mendes de Sousa A, Borralho N, Sivadon P, Grima-Pettenati J. 2005. Transcript profiling of Eucalyptus xylem genes during tension wood formation. New Phytologist 167 : 89 100.
30. Peirson SN, Butler JN, Foster RG. 2003. Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Research 3 : e73.
31. Purugganan MD. 2000. The molecular population genetics of regulatory genes. Molecular Ecology 9 : 1451 1461.
32. Remm M, Storm CEV, Sonnhammer ELL. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 314 : 1041 1052.
33. Samuels KHR, Douglas CJ, Mansfield SD, Dharmawardhana DP, Ellis BE. 2002. Cellular machinery of wood production: differentiation of secondary xylem in Pinus contorta var. latifolia. Planta 216 : 72 82.
34. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU. 2005. A gene expression map of Arabidopsis thaliana development. Nature Genetics 37 : 501 506.
35. Schrader J, Moyle R, Bhalerao R, Hertzberg M, Lundeberg J, Nilsson P, Bhalerao RP. 2004a. Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome. Plant Journal 40 : 173 187.
36. Schrader J, Nilsson J, Mellerowicz E, Berglund A, Nilsson P, Hertzberg M, Sandberg G. 2004b. A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity. Plant Cell 16 : 2278 2292.
37. Spellman PT, Rubin GM. 2002. Evidence for large domains of similarly expressed genes in the Drosophila genome. Journal of Biology 1 : 5. 1 5. 8.
38. Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences, USA 100 : 9440 9445.
39. Tautz D. 2000. Evolution of transcriptional regulation. Current Opinion in Genetics and Development 10 : 575 579.
40. Taylor G. 2002. Populus: Arabidopsis for forestry. Do we need a model tree? Annals of Botany 90 : 681 689.
41. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313 : 1596 1604.
42. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van R, De Paepe A, Speleman F. 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 3 : 0034.
43. Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA. 2003. The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution 20 : 1377 1419.
44. Zhan S, Horrocks J, Lukens LN. 2006. Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains. Plant Journal 45 : 347 357.