Showing papers by "Susan Lucas 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 Helsinki23, University of Turku24, 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
National Institutes of Health1, Birkbeck, University of London2, United States Department of Energy3, North Carolina State University4, United States Department of Agriculture5, Utah State University6, University of Nebraska–Lincoln7, University of Minnesota8, University of Wisconsin-Madison9, University of California, San Diego10, University of California, Davis11, University of Idaho12
TL;DR: Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
Abstract: Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
1,314 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: Comparison of the genomes of two members of the B. cereus group revealed differences in terms of virulence, metabolic competence, structural components, and regulatory mechanisms, as well as shared and unique genes among these isolates in comparison to the genome of pathogenic strains B. anthracis Ames and B. cerealus.
Abstract: Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains of B. anthracis reveal conspicuous sequence homogeneity, environmental isolates of B. cereus and B. thuringiensis exhibit extensive genetic diversity. Here we report the sequencing and comparative analysis of the genomes of two members of the B. cereus group, B. thuringiensis 97-27 subsp. konkukian serotype H34, isolated from a necrotic human wound, and B. cereus E33L, which was isolated from a swab of a zebra carcass in Namibia. These two strains, when analyzed by amplified fragment length polymorphism within a collection of over 300 of B. cereus, B. thuringiensis, and B. anthracis isolates, appear closely related to B. anthracis. The B. cereus E33L isolate appears to be the nearest relative to B. anthracis identified thus far. Whole-genome sequencing of B. thuringiensis 97-27and B. cereus E33L was undertaken to identify shared and unique genes among these isolates in comparison to the genomes of pathogenic strains B. anthracis Ames and B. cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus ATCC 14579. Comparison of these genomes revealed differences in terms of virulence, metabolic competence, structural components, and regulatory mechanisms.
231 citations
TL;DR: This report reports the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner, and suggests that the rearrangements leading to the sea urchin gene order were many and complex.
Abstract: While the highly consistent gene order and axial colinear patterns of expression seem to be a feature of vertebrate hox gene clusters, this pattern may be less well conserved across the rest of the bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3' gene is Hox5. (The gene order is 5'-Hox1, 2, 3, 11/13c, 11/13b, 11/13a, 9/10, 8, 7, 6, 5-3'.) The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.
145 citations
15 Feb 2006
TL;DR: Author(s): Rio, Tijana Glavina del; Harmon-Smith, Miranda; Lucas, Susan M.
Abstract: Author(s): Rio, Tijana Glavina del; Harmon-Smith, Miranda; Lucas, Susan M.; Copeland, Alex; Barry, Kerrie; Richardson, Paul; Dalin, Eileen; Tice, Hope; Shaprio, Harris; Pangilinan, Jasmyn; Bruce, David; Lapidus, Alla; Rokhsar, Daniel; Platt, Darren; Bristow, Jim
2 citations
2 citations
15 May 2006
TL;DR: Thermobifida fusca is a moderate thermophilic soil bacterium that belongs to actinobacteria that is a major degrader of plant cell walls and has a small number (39) of unique genes.
Abstract: Author(s): Kyrpides, Nikos | Abstract: Thermobifida fusca is a moderate thermophilic soil bacterium that belongs to actinobacteria. It is a major degrader of plant cell walls. Complete genome sequence showed that the T. fusca genome consists of a single circular chromosome of 3642249 bp with 85% of the genome sequence predicted to encode 3117 proteins and 65 RNA species. Genome analysis revealed the existence of 29 putative glycosyl hydrolases in addition to the 6 already identified cellulases. The glucosyl hydrolases include enzymes predicted to exhibit mainly dextran/starch and xylan degrading functions. At least two of the secreted cellulases have sequence signatures that indicate their secretion is mediated by the twin-arginine translocation system. Beside the twin-arginine translocation sysem, T. fusca possesses components of the sec system that allows proteins to cross the inner membrane and appears to lack other major secretion systems. T. fusca has the core phosphotransferase system components as other Actinobacteria but lacks PTS transporters. Genome comparisons reveal that 146 genes were laterally transferred to T. fusca. T. fusca has a small number (39) of unique genes.
1 citations