Notable Scientific Publications
May 5, 2013
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. (Nature Methods.) We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph–based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers.
March 24, 2013
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. (Nature Genetics.) Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype.
December 20, 2012
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. (Nature.) Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago, conferred about 30–36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms.
November 28, 2012
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. (Nature.) Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes.
October 8, 2012
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. (PNAS.) Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 years.
August 2, 2012
Defining the core Arabidopsis thaliana root microbiome. (Nature.) Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation.
June 29, 2012
The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. (Science.) Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species.
June 13, 2012
A framework for human microbiome research. (Nature.) The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community.
June 13, 2012
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome.
(Nature.) To characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far.
June 4, 2012
Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. (PLoS One.) A conceptual model of biogeochemical cycles and metabolic and microbial community shifts within a hot spring ecosystem via coordinated analysis of the "Bison Pool" (BP) Environmental Genome and a complementary contextual geochemical dataset of ∼75 geochemical parameters.
June 4, 2012
Fine Mapping of the Bsr1 Barley Stripe Mosaic Virus Resistance Gene in the Model Grass Brachypodium distachyon. (PLoS One.) The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals.
May 22, 2012
Artificial polyploidy improves bacterial single cell genome recovery. (PLoS One.) The method presented here shows the potential to obtain a nearly complete genome sequence from a single bacterial cell.
May 21, 2012
The metagenome of an anaerobic microbial community decomposing poplar wood chips. (PLoS One.) This study focuses on a community that developed on poplar biomass in a non-aerated bioreactor over the course of a year, with no microbial inoculation other than the naturally occurring organisms on the woody material.
May 13, 2012
Reference genome sequence of the model plant Setaria. (Nat Biotechnol.) A high-quality reference genome sequence for foxtail millet (Setaria italica) was generated. The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space.
April 18, 2012
Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals. (PLoS One.) Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodiniumform symbiotic relationships with reef-building corals and other marine invertebrates.
April 12, 2012
A Genome-Wide Survey of Switchgrass Genome Structure and Organization. (PLoS One.) Two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly.
January 9, 2012
Generation of long insert pairs using a Cre-LoxP Inverse PCR approach. (PLoS One.) A new approach, Cre-LoxP Inverse PCR Paired-End (CLIP-PE), exploits the advantages of (1) Cre-LoxP recombination system to efficiently circularize large DNA fragments, (2) inverse PCR to enrich for the desired products that contain both ends of the large DNA fragments, and (3) the use of restriction enzymes to introduce a recognizable junction site between ligated fragment ends and to improve the self-ligation efficiency.
January 2012
IMG: the integrated microbial genomes database and comparative analysis system. (Nucleic Acids Res.) The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context.
December 1, 2011 OR January 2012
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. (Nucleic Acids Res.) The Genomes OnLine Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide.
November 23, 2011
The genome of Tetranychus urticae reveals herbivorous pest adaptations (Nature) Genomic resources from the tiny two-spotted spider mite, which can extract the nutrients it needs from the leaves of more than a thousand different plant species including bioenergy feedstocks, are proving useful for multiple applications.
November 22, 2011 OR January 2012
The Genome Portal of the Department of Energy Joint Genome Institute. (Nucleic Acids Res.) The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools.
November 15, 2011 OR January 2012
IMG/M: the integrated metagenome data management and comparative analysis system. (Nucleic Acids Res.) The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context.
November 7, 2011
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw (Nature) A metagenomic analysis of the Arctic permafrost, which keeps more than 250 times the amount of greenhouse gas emissions attributed to the United States in the year 2009 out of the Earth’s atmosphere, leads to the draft genome of a novel methanogen.
October 20, 2011
Decontamination of MDA Reagents for Single Cell Whole Genome Amplification. (PLoS One.) Single cell genomics is a powerful and increasingly popular tool for studying the genetic make-up of uncultured microbes.
October 7, 2011
The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota. (PLoS One.) The complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain of the crenarchaeotal order Thermoproteales.
October 2, 2011
Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. (Nature Biotechnology) The genomes of thermophilic fungi could assist bioenergy researchers in optimizing the multistep process involved in breaking down plant biomass and then converting it into fermentable sugars that can be refined into fuel for the world’s transportation needs.
September 2, 2011
Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean. (Science.) Studies involving single-cell sorting and whole-genome amplification of several uncultured and ubiquitous microbial lineages provide new perspective on carbon cycling in the dark ocean.
August 18, 2011
Meraculous: De Novo Genome Assembly with Short Paired-End Reads. (PLoS One.) A new algorithm offers an efficient way to assemble deep paired-end short reads assemblies of eukaryotic genomes.
July 25, 2011
Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. (PNAS)
To identify genes involved in xylose metabolism for biomass conversion, a comparative genomic approach was applied across 14 Ascomycete genomes to identify genes involved in xylose metabolism.
July 14, 2011
The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi. (Science)
Comparative and functional genomics and analyses of the “dry rot” fungus Serpula lacrymans, derived from forest ancestors, identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta.
July 1, 2011
Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. (Green Chemistry.)
The identification of enzymes that can tolerate ionic liquids that could be produced as a cellulase cocktail would reduce the costs and water use requirements of the biomass pretreatment process.
June 30, 2011
Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies. (Science.)
A dominant bacterial species (WG-1) from the Tammar wallaby microbiota implicated in lower methane emissions with starch containing diets provides new strategic targets for redirecting fermentation and reducing methane production in livestock.
May 5, 2011
The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. (Science.)Among other things, the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported, revealed that the transition from a gametophyte- to sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant.
May 4, 2011
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. (Genome Research.) The 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.
May 2, 2011
Obligate biotrophy features unraveled by the genomic analysis of rust fungi. (PNAS.) As rust fungi are some of the most devastating pathogens of crop plants, the DOE JGI sequenced Melampsora larici-populina, the causal agent of poplar leaf rust, and then compared it to the genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust.
February 23, 2011
Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. (PNAS.) A comparison of the genome of the harmful alga Aureococcus anophagefferens with six competing phytoplankton species identified gene sets that explain how brown tide dominates within the environmental conditions present during algal blooms.
February 4, 2011
The Ecoresponsive Genome of Daphnia pulex. (Science) Daphnia pulex, or the water flea, is a keystone species of freshwater ecosystems: a principal grazer of algae, a primary forage for fish, and a sentinel of lentic (still water) inland ecosystems.
January 28, 2011
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen. (Science) 268 gigabases of metagenomic sequence data from the microbiota in cow rumen to identify genes and genomes participating in biomass deconstruction.
December 21, 2010
From the Cover: Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. (Proc Natl Acad Sci U S A). The genome of soybean (Glycine max), a commercially important crop, has recently been sequenced and now the genome sequence of G. soja, the undomesticated ancestor of G. max is available.
November 29, 2010
Multiple displacement amplification compromises quantitative analysis of metagenomes. (Nat Methods).
November 15, 2010
Comparative genomics of clinical and environmental Vibrio mimicus. (Proc Natl Acad Sci U S A). The objective of this study was to determine the genetic basis of V. mimicus physiology, pathogenicity, and evolution and to clarify its relationship with V. cholerae.
September 23, 2010
An insect herbivore microbiome with high plant biomass-degrading capacity. (PLoS Genet). The fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity.
September 21, 2010
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. (Proc Natl Acad Sci U S A). Marine dissolved organic matter (DOM) contains as much carbon as the Earth's atmosphere, and represents a critical component of the global carbon cycle.
September 19, 2010
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. (Nat Methods). The effectiveness and fidelity of subtractive hybridization and exonuclease digestion, as well as combinations of these treatments, on two synthetic five-microorganism metatranscriptomes using massively parallel sequencing, were validated.
August 22, 2010
ChIP-Seq identification of weakly conserved heart enhancers. (Nat Genet). The evolutionary conservation of embryonic enhancers can vary depending on tissue type.
August 17, 2010
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. (Proc Natl Acad Sci U S A). Metagenomic and bioinformatic approaches were used to characterize plant biomass conversion within the foregut microbiome of Australia's "model" marsupial, the Tammar wallaby (Macropus eugenii)
August 17, 2010
Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. (Proc Natl Acad Sci U S A). Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes.
August 16, 2010
The United States of America and scientific research. (PLoS One). This study's aim is to facilitate a serious discussion of key questions by the research community and federal policy makers.
August 10, 2010
Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. (PLoS Biol).The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations.
August 5, 2010
The Amphimedon queenslandica genome and the evolution of animal complexity. (Nature). Amphimedon queenslandica, a demosponge from the Great Barrier Reef turns out to be remarkably similar to other animal genomes in content, structure and organization.
July 11, 2010
Genome sequence of the model mushroom Schizophyllum commune. (Nat Biotechnol). The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass.
July 9, 2010
Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. (Sciene). The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development.
July 8, 2010
Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. (PLoS One). An ancient cyanobacterial incorporation into a eukaryotic organism led to the evolution of plastids (chloroplasts) and subsequently to the origin of the plant kingdom.
May 21, 2010
A Catalog of Reference Genomes from the Human Microbiome (Science) The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body.
May 11, 2010
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea (PNAS) Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling.
May 5, 2010
The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. (PLoS One). Many bacteria in the environment have adapted to the presence of toxic heavy metals and this has been the subject of extensive research over the last 30 years.
May 2, 2010
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. (Nature Methods) For any genome, gene-finding is the key step to understanding the biochemistry, physiology and ecology of the organism.
April 30, 2010
The genome of the Western clawed frog Xenopus tropicalis. (Science) The species Xenopus laevis was first introduced to the United States in the 1940s where a low-cost pregnancy test took advantage of the responsiveness of frogs to human chorionic gonadotropin.
April 23, 2010
One bacterial cell, one complete genome. (PLoS One) Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell.
April 16, 2010
Evolution of an expanded sex-determining locus in Volvox. (Science). The mating locus (MT) of the sexually dimorphic multicellular green alga Volvox carteri specifies the production of eggs and sperm and has undergone a remarkable expansion and divergence relative to MT from Chlamydomonas reinhardtii, which is a closely related unicellular species.
April 16, 2010
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community (PLoS One) Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions.
March 22, 2010
The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader. (PLoS One) upriavidus necator JMP134 is a Gram-negative β-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.
March 18, 2010
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. (Nature). Fusarium species are among the most important phytopathogenic and toxigenic fungi and the genomes of three phenotypically diverse species were compared.
March 14, 2010
The dynamic genome of hydra (Nature) The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years.
March 5, 2010
The genome of Naegleria gruberi illuminates early eukaryotic versatility (Cell). The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing the identification of thousands of genes likely present in the pan-eukaryotic ancestor.
February 19, 2010
The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database (PLoS One) With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation.
February 11, 2010
Genome sequencing and analysis of the model grass Brachypodium distachyon.(Nature). Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat.
February 5, 2010
Close association of RNA polymerase II and many transcription factors with Pol III genes (PNAS) Transcription of the eukaryotic genomes is carried out by three distinct RNA polymerases I, II, and III, whereby each polymerase is thought to independently transcribe a distinct set of genes.
February 3, 2010
Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp tularensis A1 and Schu S4 (PLoS One) Francisella tularensis subspecies tularensis consists of two separate populations A1 and A2.
January 21, 2010
Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community (PLoS One) Tailoring depolymerizing enzymes to particular feedstocks and pretreatment conditions is one promising avenue of research in cellulosic biofuels.
January 15, 2010
Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. (Science). How major expression and morphological changes can arise from single mutational leaps in natural populations, producing new adaptive alleles via recurrent regulatory alterations in a key developmental control gene.
January 14, 2010
Genome sequence of the palaeopolyploid soybean. (Nature) Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms.
January 2010
A restricted spectrum of NRAS mutations causes Noonan syndrome (Nature Genetics) Noonan syndrome, a developmental disorder characterized by congenital heart defects, reduced growth, facial dysmorphism and variable cognitive deficits, is caused by constitutional dysregulation of the RAS-MAPK signaling pathway.
December 24, 2009
A phylogeny-driven genomic encyclopedia of bacteria and archaea. (Nature). Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms.
November 24, 2009
Gene Context Data Analysis in the Integrated Microbial Genomes (IMG) Data Management System. (PLoS ONE). Function prediction methods can be extended using gene context analysis approaches such as examining the conservation of chromosomal gene clusters, gene fusion events and co-occurrence profiles across genomes.
November 5, 2009
Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. (PLoS Genetics) Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant.
October 23, 2009
Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones. (Science). A metagenomic analyses of a ubiquitous and abundant but uncultivated oxygen minimum zone microbe (SUP05).
October 9, 2009
Genomics: Genome project standards in a new era of sequencing. (Science). Ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole-genome sequencing that requires reevaluation of such standards.
September 10, 2009
Prepublication data sharing. (Nature). With the advent of methods for large-scale and high-throughput data analyses, the generation and transmission of the underlying facts are often replaced by an electronic process that involves sending information to and from scientific databases.
September 10, 2009
Genomic views of distant-acting enhancers. (Nature) A great number of recent genome-wide association studies suggest that non-coding variation is a significant risk factor for common disorders, but the mechanisms by which this variation contributes to disease remain largely obscure.
September 8, 2009
Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. (PNAS). Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat.
August 5, 2009
The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. (PLoS Genetics) The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of more than 50 species known as the “Fusarium solani species complex”.
June 5, 2009
Molecular Evolutionary Consequences of Niche Restriction in Francisella tularensis, a Facultative Intracellular Pathogen. (PLoS Pathogens). Francisella tularensis is a potent mammalian pathogen well adapted to intracellular habitats, whereas F. novicida and F. philomiragia are less virulent in mammals and appear to have less specialized lifecycles.
June 4, 2009
Genomic characterization of methanomicrobiales reveals three classes of methanogens. (PLoS One). Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens.
April 23, 2009
Assembling the marine metagenome, one cell at a time. (PLoS One). The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches.
February 12, 2009
ChIP-seq accurately predicts tissue-specific activity of enhancers. (Nature).
A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes.
February 5, 2009
Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. (PLoS Genetics) Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life.
January 29, 2009
The Sorghum bicolor genome and the diversification of grasses. (Nature) Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel.
January 16, 2009
Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. (PLoS One). T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols.
January 15, 2009
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii.( PLoS One). Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake.
December 2008
Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease (Nature Genetics) Nonalcoholic fatty liver disease (NAFLD) is a burgeoning health problem of unknown etiology that varies in prevalence among ancestry groups.
December 2, 2008
The genome sequence of Bifidobacterium longum subsp infantis reveals adaptations for milk utilization within the infant microbiome (PNAS) Following birth, the breast-fed infant gastrointestinal tract is rapidlycolonized by a microbial consortium often dominated by bifidobacteria.
November 25, 2008
Intergenic Locations of Rice Centromeric Chromatin (PLoS Biology) Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis.
October 30, 2008
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals (Nature) In bilaterian animals, such as humans, flies and worms, hundreds of microRNAs (miRNAs), some conserved throughout bilaterian evolution, collectively regulate a substantial fraction of the transcriptome.
October 21, 2008
Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers (PNAS) We have performed a genome-wide analysis of copy number changes in breast and colorectal tumors using approaches that can reliably detect homozygous deletions and amplifications.
September 30, 2008
Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism (PNAS) We have established Meloidogyne hapla as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and we present a complete genome sequence.
September 25, 2008
Microbiology - Metagenomics (Nature) Meta genomics provides a relatively unbiased view not only of the community structure (species richness and distribution) but also of the functional (metabolic) potential of a community
September 5, 2008
Human-specific gain of function in a developmental enhancer (Science) Changes in gene regulation are thought to have contributed to the evolution of human development.
September 2008
Protein-based organelles in bacteria: carboxysomes and related microcompartments (Nature Reviews Microbiology) Many bacteria contain intracellular microcompartments with outer shells that arecomposed of thousands of protein subunits and interiors that are filled with functionally related enzymes.
August 21, 2008
The Trichoplax genome and the nature of placozoans (Nature) As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood.
August 19, 2008
A photoactive carotenoid protein acting as light intensity sensor (PNAS) Intense sunlight is dangerous for photosynthetic organisms. Cyanobacteria, like plants, protect themselves from light-induced stress by dissipating excess absorbed energy as heat.
August 17, 2008
High-resolution metagenomics targets specific functional types in complex microbial communities (Nature Biotechnology) We developed a method to target microbial subpopulations by labeling DNA through stable isotope probing (SIP), followed by WGS sequencing.
August 14, 2008
Genomics of cellulosic biofuels (Nature)
Cellulosic biomass has then potential to contribute to meeting the demand for liquid fuel, but land-use requirements and process inefficiencies represent hurdles for large-scale deployment of biomass-to-biofuel technologies.
July 11, 2008
Paleontology - New tricks with old bones (Science) Progress in the field of ancient-organism genomics is prying open doors into the tombs of the long-deceased relatives of humans and other mammals.
July 9, 2008
A molecular study of microbe transfer between distant environments. (PLoS One) In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances.
June 19, 2008
The amphioxus genome and the evolution of the chordate karyotype (Nature) Lancelets (‘amphioxus’) are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period.
June 6 2008
The transcription/migration interface in heart precursors of Ciona intestinalis (Science) Gene regulatory networks direct the progressive determination of cell fate during embryogenesis, but how they control cell behavior during morphogenesis remains largely elusive.
June 3, 2008
Promoter elements associated with RNA Pol 11 stalling in the Drosophila embryo
(PNAS) Here, we present a combined computational and experimental analysis of stalled promoters to determine how they come to bind Pol II in the early Drosophila embryo.
May 30, 2008
Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40(T) (PLoS Genetics) The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides.
May 8, 2008
The minimum information about a genome sequence (MIGS) specification (Nature Biotechnology) With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format.
April 2, 2008
The Airborne Metagenome in an Indoor Urban Environment (PLoS One) Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches
March 2008
CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea (Nature Reviews Microbiology) Arrays of clustered, regularly interspaced short palindromic repeats (CRISPRs) are widespread in the genomes of many bacteria and almost all archaea.
February 22, 2008
Atomic-level models of the bacterial carboxysome shell (Science) The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation.
January 23, 2008
Group II Introns Break New Boundaries: Presence in a Bilaterian's Genome (PLoS One) Reports that the first group II intron found in the mitochondrial genome of a bilaterian worm holds implications for understanding mechanisms, constraints, and selective pressures that account for patterns of animal mitochondrial genome evolution
January 4, 2008
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants (Science) The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant’s unique facility for reverse genetics.
May 4, 2008
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). (Nature Biotechnology) Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol.
March 6, 2008
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. (Nature) Mycorrhizal symbioses—the union of roots and soil fungi—are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants.
February 14, 2008
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. (Nature) Choanoflagellates have long fascinated evolutionary biologists for their marked similarity to the 'feeding cells' (choanocytes) of sponges and the possibility that they might represent the closest living relatives of metazoans.
January 6, 2008
Ultraconservation identifies a small subset of extremely constrained developmental enhancers. (Nature Genetics) Extended perfect human-rodent sequence identity of at least 200 base pairs (ultraconservation) is potentially indicative of evolutionary or functional uniqueness.
December 13, 2007
The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. (Science) We report the draft genome sequence of the model moss Physcomitrella patens and compare its features to those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae.
November 22, 2007
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. (Nature) The first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation.
October 18, 2007
Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer. (Science Express) Our data suggest that toxicity to the host inhibited transfer regardless of the species of origin and that increased gene dosage and associated increased expression may be a predominant cause for transfer failure.
October 12, 2007
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions. (Science) Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
September 26, 2007
Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks. (PLoS One) . . . we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes.
September 4, 2007
Deletion of Ultraconserved Elements Yields Viable Mice. (PLoS Biology) Lines of mice lacking ultraconserved elements were viable and fertile, and failed to reveal any critical abnormalities when assayed for a variety of phenotypes including growth, longevity, pathology, and metabolism.
July 6, 2007
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization. (Science) Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis.
June 11, 2007
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. (PNAS) Our analysis shows that S. tropica dedicates a large percentage of its genome ({approx}9.9%) to natural product assembly, which is greater than previous Streptomyces genome sequences as well as other natural product-producing actinomycetes.
May 1, 2007
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. (PNAS) The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species . . .
April 29, 2007
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. (Nature Methods) To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes.
March 7, 2007
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. (Nature) Here we use community genomic data sets to identify, with strain specificity, expressed proteins from the dominant member of a genomically uncharacterized, natural, acidophilic biofilm.
March 4, 2007
Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. (Nature Biotechnology) Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast.
February 25 , 2007
Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. (Nature Genetics) Resequencing of ANGPTL4 in a multiethnic population allowed analysis of the phenotypic effects of both rare and common variants while taking advantage of genetic variation arising from ethnic differences in population history.
February 23, 2007
Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments. (Science) We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA–based approaches depending on the polymerase chain reaction.
February 16, 2007
The Calyptogena magnifica Chemoautotrophic Symbiont Genome. (Science) The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities.
February 1, 2007
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. (Nature Biotechnology) The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains.
November 3, 2006
Accelerated Evolution of Conserved Noncoding Sequences in Humans. (Science) We identified 992 conserved noncoding sequences (CNSs) with a significant excess of human-specific substitutions. These accelerated elements were disproportionately found near genes involved in neuronal cell adhesion.
October 9, 2006
Comparative Genomics of Lactic Acid Bacteria. (PNAS) 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.
September 25, 2006
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. (Nature Biotechnology) Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, "Candidatus Accumulibacter phosphatis."
September 18, 2006
Symbiosis insights through metagenomic analysis of a microbial consortium. (Nature) Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis.
September 15, 2006
The Genome of Black Cottonwood, Populus
trichocarpa (Torr. & Gray) (Science) 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.
September 1, 2006
Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis (Science) Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum . . . Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection . . .
May, 2006
Computational analysis
of the Phanerochaete
chrysosporium v2.0 genome database and mass spectrometry identification
of peptides in ligninolytic cultures reveal complex mixtures of secreted
proteins (Fungal
Genetics and Biology) The white-rot basidiomycete Phanerochaete
chrysosporium employs
extracellular enzymes to completely degrade the major polymers of wood:
cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1
gene models predicts 769 secreted proteins, a substantial increase over
the 268 models identified in the earlier database . . .
September 12, 2005
Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate (PLoS Biology) We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene duplicated relative to the evolutionary tree of the organisms. . . [T]heir global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution.
July 2, 2005
The Phanerochaete chrysosporium secretome:
Database predictions and initial mass spectrometry peptide identifications
in cellulose-grown medium (Journal
of Biotechnology) The white rot basidiomycete, Phanerochaete
chrysosporium, employs an array of extracellular enzymes to
completely degrade the major polymers of wood: cellulose, hemicellulose
and lignin. Towards the identification of participating enzymes, 268
likely secreted proteins were predicted using SignalP and TargetP algorithms.
June 2, 2005
Genomic Sequencing of Pleistocene Cave Bears (Science Express)
Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to amplification of mitochondrial sequences. We describe metagenomic libraries constructed using unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears.
April 22, 2005
Comparative Metagenomics of Microbial Communities (Science) The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.
December 23 , 2004
The sequence and analysis of duplication-rich human chromosome 16 (Nature) Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin.
October 21, 2004
Megabase deletions of gene deserts result in viable mice (Nature) The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism.
Finishing the euchromatic sequence of the human genome (Nature) In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage.
October 1, 2004
The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism (Science) Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for ~20% of global carbon fixation. We report the 34 million–base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand–base pair plastid and 44 thousand–base pair mitochondrial genomes.
September 15, 2004
The DNA sequence and comparative analysis of human chromosome 5 (Nature) Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities.
September 3 , 2004
Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics (Science) Nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs. These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation.
May 2, 2004
Genome sequence of the lignocellulose degrading fungusPhanerochaete chrysosporium strain RP78 (Nature Biotechnology) The P. chrysosporium genome reveals an impressive array of genes encoding secreted oxidases, peroxidases and hydrolytic enzymes that cooperate in wood decay. Analysis of the genome data will enhance our understanding of lignocellulose degradation, a pivotal process in the global carbon cycle, and provide a framework for further development of bioprocesses for biomass utilization, organopollutant degradation and fiber bleaching. This genome provides a high quality draft sequence of a basidiomycete, a major fungal phylum that includes important plant and animal pathogens.
April 1 , 2004
The DNA Sequence and Biology of Human Chromosome 19 (Nature) The finished human chromosome 19 sequence, comprising a gene density more than double the genome-wide average, marks the culmination of 18 years of research spanning the history of modern genomics.
February 1, 2004
Community Structure and Metabolism through Reconstruction of Microbial Genomes from the Environment (Nature AOP) Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes.
October 17, 2003
Scanning Human Gene Deserts for Long-Range Enhancers (Science 302: 413) Approximately 25% of the genome consists of gene-poor regions greater than 500 kb, termed gene deserts. These segments have been minimally explored, and their functional significance remains elusive. One category of functional sequences postulated to lie in gene deserts is gene regulatory elements that have the ability to modulate gene expression over very long distances.
March 21, 2003
Hexapod Origins: Monophyletic or Paraphyletic? (Science 299: 1887-1889) Recent morphological and molecular evidence has changed interpretations of arthropod phylogeny and evolution. Here we compare complete mitochondrial genomes to show that Collembola, a wingless group traditionally considered as basal to all insects, appears instead to constitute a separate evolutionary lineage that branched much earlier than the separation of many crustaceans and insects and independently adapted to life on land. Therefore, the taxon Hexapoda, as commonly defined to include all six-legged arthropods, is not monophyletic.
February 28, 2003
Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome (Science 299: 1391-1394) Nonhuman primates represent the most relevant model organisms to understand the biology of Homo sapiens. The recent divergence and associated overall sequence conservation between individual members of this taxon have nonetheless largely precluded the use of primates in comparative sequence studies.
December 12, 2002
The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins (Science 298: 2157-2167) The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates.
August 23, 2002
Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes (Science 297: 1301-1310) The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds.
July 6, 2001
Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution (Science 293: 104-111) The JGI team's analysis permitted more than 1200 HSA19 genes to be verified or defined and revealed clues to the evolutionary history of this gene-rich human chromosome. This first chromosome-wide comparative sequencing study also provides a preview of how the whole mouse genome sequence will aid in discovery of genes and other functional DNA sequences throughout all 23 sets of human chromosomes.
February 15, 2001
Initial sequencing and analysis of the human genome. (Nature 409: 860-921) The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
