title: Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms.
abstract: Sequencing of the Populus trichocarpa genome creates an opportunity to describe the transcriptome of a woody perennial species and establish an atlas of gene expression. A comparison with the transcriptomes of other species can also define genes that are conserved or diverging in plant species. Here, the transcriptome in vegetative organs of the P. trichocarpa reference genotype Nisqually-1 was characterized. A comparison with Arabidopsis thaliana orthologs was used to distinguish gene functional categories that may be evolving differently in a woody perennial and an annual herbaceous species. A core set of genes expressed in common among vegetative organs was detected, as well as organ-specific genes. Statistical tests identified chromatin domains, where adjacent genes were expressed more frequently than expected by chance. Extensive divergence was detected in the expression patterns of A. thaliana and P. trichocarpa orthologs, but transcription of a small number of genes appeared to have remained conserved in the two species. Despite separation of lineages for over 100 million yr, these results suggest that selection has limited transcriptional divergence of genes associated with some essential functions in A. thaliana and P. trichocarpa. However, extensive remodeling of transcriptional networks indicates that expression regulation may be a key determinant of plant diversity.
authors.affiliation: Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL 32611, USA.|School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL 32611, USA.
authors.forename: Tania
authors.initials: T
authors.lastname: Quesada
authors.affiliation: Department of Statistics, University of Florida, PO Box 118545, Gainesville, FL 32611-8545, USA.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Li
authors.affiliation: School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL 32611, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Dervinis
authors.affiliation: Department of Statistics, University of Florida, PO Box 118545, Gainesville, FL 32611-8545, USA.
authors.forename: Yao
authors.initials: Y
authors.lastname: Li
authors.affiliation: Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL 32611, USA.|School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL 32611, USA.
authors.forename: Philip N
authors.initials: PN
authors.lastname: Bocock
authors.affiliation: Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA.|Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr, Knoxville, TN, 37996-4561, USA.
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
authors.affiliation: Department of Statistics, University of Florida, PO Box 118545, Gainesville, FL 32611-8545, USA.|University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL 32610-3610, USA.
authors.forename: George
authors.initials: G
authors.lastname: Casella
authors.affiliation: Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL 32611, USA.|School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL 32611, USA.|University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL 32610-3610, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Davis
authors.affiliation: Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL 32611, USA.|School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL 32611, USA.|University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL 32610-3610, USA.
authors.forename: Matias
authors.initials: M
authors.lastname: Kirst
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics; D018514:Plant Structures / Q000235:genetics; D032107:Populus / Q000235:genetics*