Showing papers by "Susan Lucas published in 2011"
Indiana University1, University of Notre Dame2, Utah State University3, University of New Hampshire4, University of California, Santa Barbara5, University of Tokyo6, United States Department of Energy7, Ludwig Maximilian University of Munich8, National Institutes of Health9, J. Craig Venter Institute10, University of Illinois at Urbana–Champaign11, Hebrew University of Jerusalem12, University of North Texas13, Harvard University14, University of Geneva15, Research Institute of Molecular Pathology16, Oregon State University17, Utrecht University18, University of California, Davis19, Hoffmann-La Roche20, University of Iowa21, University of Strasbourg22, University of Washington23, University of Texas at Arlington24, University of California, Santa Cruz25, Life Technologies26, New York University27, University of Guelph28, Imperial College London29, University of California, Berkeley30
TL;DR: The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions, and the coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random.
Abstract: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.
1,204 citations
Purdue University1, Kanazawa University2, Graduate University for Advanced Studies3, National Institutes of Natural Sciences, Japan4, Monash University5, University of California, Davis6, Pennsylvania State University7, University at Buffalo8, New York Botanical Garden9, University of Regina10, University of Arizona11, University of Georgia12, University of Potsdam13, Salk Institute for Biological Studies14, Charles University in Prague15, College of William & Mary16, University of California, San Diego17, École normale supérieure de Lyon18, Carnegie Institution for Science19, Hokkaido University20, University of Jena21, Martin Luther University of Halle-Wittenberg22, University of Copenhagen23, University of Tokyo24, Nagoya University25, Free University of Berlin26, University of Tsukuba27, University of Tübingen28, University of Rostock29, Nara Institute of Science and Technology30, Mayo Clinic31, University of California, Berkeley32, Rutgers University33, National Institute of Genetics34, Max Planck Society35, University of Tennessee Health Science Center36, University of Washington37, Dalhousie University38, University of Oxford39, University of Freiburg40, University of Los Andes41, University of Rhode Island42, Joint BioEnergy Institute43, Ruhr University Bochum44, Texas A&M University45, Osaka University46, Cornell University47, Cold Spring Harbor Laboratory48, University of Burgundy49, Utah State University50, United States Department of Energy51
TL;DR: The genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported, is reported, finding that the transition from a gametophytes- to a sporophyte-dominated life cycle required far fewer new genes than the Transition from a non Seed vascular to a flowering plant.
Abstract: Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
750 citations
Institut national de la recherche agronomique1, Harvard University2, United States Department of Energy3, University of Upper Alsace4, Natural Resources Canada5, Max Planck Society6, Aix-Marseille University7, University of British Columbia8, Hoffmann-La Roche9, University of Göttingen10, Commonwealth Scientific and Industrial Research Organisation11, University of Sydney12, Oak Ridge National Laboratory13, North Dakota State University14, University of Minnesota15
TL;DR: The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition.
Abstract: Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.
605 citations
Swansea University1, Clark University2, University of Göttingen3, Schiller International University4, United States Department of Energy5, University of Helsinki6, Pacific Northwest National Laboratory7, American Museum of Natural History8, University of Maine9, University of Provence10, Royal Netherlands Academy of Arts and Sciences11, Southeast Missouri State University12, Virginia Tech13, Swedish University of Agricultural Sciences14, University of Oslo15, Institut national de la recherche agronomique16, Universidad Pública de Navarra17, Seoul National University18, University of Hamburg19, University of Oxford20
TL;DR: Fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota through convergent evolution and divergence among fungal decomposers.
Abstract: Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.
522 citations
Novozymes1, United States Department of Energy2, Concordia University3, Aix-Marseille University4, University of New Mexico5, Utrecht University6, Centraalbureau voor Schimmelcultures7, Sandia National Laboratories8, Macquarie University9, Pacific Northwest National Laboratory10, McGill University11, University of Glasgow12, Broad Institute13
TL;DR: These genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi and suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass.
Abstract: Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.
430 citations
10 May 2011
TL;DR: The dramatic upregulation of transcripts coding for SSPs, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition.
378 citations
Technical University of Denmark1, DSM2, Pacific Northwest National Laboratory3, Biomax Informatics AG4, Novozymes5, University of Göttingen6, University of Seville7, Concordia University8, Chr. Hansen9, United States Department of Energy10, Stanford University11, Vienna University of Technology12, Los Alamos National Laboratory13
TL;DR: In this article, the authors performed whole-genome sequencing of the Aspergillus niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality.
Abstract: The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
308 citations
29 Apr 2011
TL;DR: In this paper, the authors performed whole-genome sequencing of the Aspergillus niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality.
Abstract: The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
306 citations
TL;DR: Several genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology.
Abstract: Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermentations. To better understand xylose utilization for subsequent microbial engineering, we sequenced the genomes of two xylose-fermenting, beetle-associated fungi, Spathaspora passalidarum and Candida tenuis. To identify genes involved in xylose metabolism, we applied a comparative genomic approach across 14 Ascomycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption phenotypes. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology.
165 citations
TL;DR: The 3.7-Mb genome sequence is presented to provide insights into the physiology of Desulfovibrio alaskensis G20 to reduce toxic radionuclides and metals to sparingly soluble and less toxic forms.
Abstract: Desulfovibrio alaskensis G20 (formerly desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7 Mb genome sequence to provide insights into its physiology.
57 citations
TL;DR: The genome of Opitutus terrae PB90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from plant-derived polysaccharides is sequenced.
Abstract: Bacteria of the deeply branching phylum Verrucomicrobia are rarely cultured yet commonly detected in metagenomic libraries from aquatic, terrestrial, and intestinal environments. We have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from plant-derived polysaccharides.
University of Helsinki1, Wageningen University and Research Centre2, Lawrence Livermore National Laboratory3, Joint Genome Institute4, Lawrence Berkeley National Laboratory5, Los Alamos National Laboratory6, Oak Ridge National Laboratory7, Commonwealth Scientific and Industrial Research Organisation8, AgResearch9
TL;DR: Chthoniobacter flavus Ellin428 is the first isolate from the class Spartobacteria of the bacterial phylum Verrucomicrobia and can metabolize many of the saccharide components of plant biomass but is incapable of growth on amino acids or organic acids other than pyruvate.
Abstract: Chthoniobacter flavus Ellin428 is the first isolate from the class Spartobacteria of the bacterial phylum Verrucomicrobia. C. flavus Ellin428 can metabolize many of the saccharide components of plant biomass but is incapable of growth on amino acids or organic acids other than pyruvate.
TL;DR: The 3.8-Mb genome sequence is presented to provide further insight into microbial mercury methylation and to investigate the mechanism of methylation by this and other organisms.
Abstract: Desulfovibrio desulfuricans strain ND132 is an anaerobic sulfate-reducing bacterium (SRB) capable of producing methylmercury (MeHg), a potent human neurotoxin. The mechanism of methylation by this and other organisms is unknown. We present the 3.8-Mb genome sequence to provide further insight into microbial mercury methylation.
01 Jan 2011
TL;DR: In this paper, the authors presented the genome of strain Exiguobacterium sp. AT1b (ATCC BAA-1283), a thermophilic, facultative anaerobic bacterium isolated from a slightly alkaline, highly carbonate hot spring water sample from Angel Terrace.
Abstract: Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physicochemical gradient. This genome was sequenced to be a comparative resource for the study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy’s (DOE’s) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/). Exiguobacterium sp. AT1b ( ATCC BAA-1283) is a thermophilic, facultative anaerobic bacterium isolated from a slightly alkaline, highly carbonate hot spring water sample from Angel Terrace, which is part of Mammoth Terrace, Yellowstone National Park. The non-spore-forming, low-GC,
University of Helsinki1, Wageningen University and Research Centre2, Commonwealth Scientific and Industrial Research Organisation3, Lawrence Livermore National Laboratory4, Joint Genome Institute5, Lawrence Berkeley National Laboratory6, Los Alamos National Laboratory7, Oak Ridge National Laboratory8, AgResearch9
TL;DR: Elin514 is an aerobically grown verrucomicrobial isolate from pasture soil that is one of the few cultured representatives of subdivision 3 of the phylum Verrucomicrobia.
Abstract: "Pedosphaera parvula" Ellin514 is an aerobically grown verrucomicrobial isolate from pasture soil. It is one of the few cultured representatives of subdivision 3 of the phylum Verrucomicrobia. Members of this group are widespread in terrestrial environments.
TL;DR: Fluviicola taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome and the inability of this freshwater bacterium to grow in the presence of Na+ ions.
Abstract: Fluviicola taffensis O’Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262T forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na+ ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na+ ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
TL;DR: Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel phylum Lentisphaerae, a deep-branching bacterial lineage, and represents an important organism for evolutionary studies.
Abstract: Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and V. vadensis therefore represents an important organism for evolutionary studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human gastrointestinal tract.
01 Jan 2011
01 Jan 2011
TL;DR: Phylogenies inferred from the 16S rRNA gene and predicted amino acid sequences of various conserved proteins indicate that JAD2 is the first cultivated representative of the GAL35 group, a new class within the Chloroflexi.
Abstract: A thermophilic, facultatively microaerophilic, heterotrophic bacterium, designated strain JAD2, was isolated from sediments of Great Boiling Spring (GBS), an ~80oC, circumneutral hot spring in the US Great Basin (GB). The strain grew anaerobically on yeast extract or peptone with an optimal growth temperature of 70-75oC. Growth was stimulated by addition of 0.01 atm O2 to the culture vessel headspace, but was inhibited by higher concentrations (0.2 atm). Cells of JAD2 formed non-motile filaments ranging from 10 to >300 μm in length, which typically decreased in length during stationary phase. 16S rRNA gene-targeted pyrotag sequencing and clone library data suggest that close relatives of this isolate are prominent members of the sediment communities in GBS. Shotgun sequencing of the JAD2 genome produced an assembly consisting of ~3.2 Mbp with an average G+C content of 67.3%. Phylogenies inferred from the 16S rRNA gene and predicted amino acid sequences of various conserved proteins indicate that JAD2 is the first cultivated representative of the GAL35 group, a new class within the Chloroflexi. Predicted genes in the draft genome encoding a putative carbon monoxide dehydrogenase (coxMSL), nitrite reductase (nrfHA) and nitrous oxide reductase (nosZ) suggest that this isolate may play important roles in N and C cycling in GBS sediments.
01 Jan 2011
TL;DR: The complete Genome Sequence of the Cellulolytic Thermophile Clostridium thermocellum DSM1313 is published for the first time.
Abstract: Feinberg, Lawrence; Foden, Justine; Barrett, Trisha; Davenport, Karen Walston; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Lapidus, Alla; Lucas, Susan; Cheng, Jan-Fang; Pitluck, Samuel; Woyke, Tanja; Ivanova, Natalia; Mikhailova, Natalia; Land, Miriam; Hauser, Loren; Argyros, D. Aaron; Goodwin, Lynne; Hogsett, David; and Caiazza, Nicky, "Complete Genome Sequence of the Cellulolytic Thermophile Clostridium thermocellum DSM1313" (2011). US Department of Energy Publications. 288. https://digitalcommons.unl.edu/usdoepub/288