Showing papers by "Richard A. Jorgensen published in 2006"
Oak Ridge National Laboratory1, University of Tennessee2, West Virginia University3, Umeå University4, University of British Columbia5, United States Department of Energy6, Ghent University7, Swedish University of Agricultural Sciences8, Institut national de la recherche agronomique9, Virginia Tech10, Michigan Technological University11, University of Toronto12, Pennsylvania State University13, University of Provence14, University of Georgia15, University of Florida16, University of California, Berkeley17, Lawrence Berkeley National Laboratory18, University of Arizona19, Purdue University20, Stanford University21, United States Department of Agriculture22, University of Turku23, University of Helsinki24, Massachusetts Institute of Technology25, University of Tennessee Health Science Center26, University of Tübingen27
TL;DR: The draft genome of the black cottonwood tree, Populus trichocarpa, has been reported in this paper, with more than 45,000 putative protein-coding genes identified.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
4,025 citations
01 Sep 2006
TL;DR: Analyzing the draft genome of the black cottonwood tree, Populus trichocarpa, revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
355 citations
TL;DR: It is reported here that antisense transgenes altered by removal of nonsense codons generate silencing patterns characteristic of sense-RNAi, and it is inferred that the latter class is due to systemic RNA silencing signals that interact with certain epigenetic states of the transgene to imprint it with information generated at a distance elsewhere in the plant.
Abstract: We describe features of RNA silencing and associated epigenetic imprints that illustrate potential roles for RNA interference (RNAi) in maintenance and transmission of epigenetic states between cells, throughout a plant, and perhaps even across sexual generations. Three types of transgenes can trigger RNAi of homologous endogenous plant genes: (1) “sense” transgenes that overexpress translatable transcripts, (2) inverted repeat (IR) transgenes that produce double-stranded RNA (dsRNA), and (3) antisense transgenes. Each mode of RNAi produces a different characteristic developmental silencing pattern. Single-copy transgenes are sufficient for sense-RNAi and antisense-RNAi, but not inverted repeat-RNAi. A single premature termination codon dramatically attenuates sense-RNAi, but it has no effect on antisense or inverted repeat-RNAi. We report here that antisense transgenes altered by removal of nonsense codons generate silencing patterns characteristic of sense-RNAi. Duplication of a sense overexpression transgene results in two types of epigenetic events: (1) complete loss of silencing and (2) altered developmental pattern of silencing. We also report that duplicating only the transgene promoter results in complete loss of silencing, whereas duplicating only transcribed sequences produces the second class, which are vein-based patterns. We infer that the latter class is due to systemic RNA silencing signals that interact with certain epigenetic states of the transgene to imprint it with information generated at a distance elsewhere in the plant.
22 citations
TL;DR: These two animations illustrate movement of a protein through an individual plasmodesma and an experiment to detect the movement of the transcription factor throughplasmodesmata from the L1 layer of a plant meristem into the L2 and L3 layers.
Abstract: Plasmodesmata are intercellular organelles in plants that allow the passage of molecules between plant cells. Movement through plasmodesmata may allow transcription factors expressed in one cell to move into adjacent cells, thereby regulating gene expression non-cell autonomously. The two animations illustrate (i) movement of a protein through an individual plasmodesma and (ii) an experiment to detect the movement of the transcription factor through plasmodesmata from the L1 layer of a plant meristem into the L2 and L3 layers. These two animations would be useful in teaching plant biology or plant development or a cell biology class discussing mechanisms of intercellular transport.
5 citations