Nicholas H. Putnam
A5060151593- Genomics and Phylogenetic Studies
- Marine Ecology and Invasive Species
- Chromosomal and Genetic Variations
- Protist diversity and phylogeny
- Parasite Biology and Host Interactions
- Genomics and Chromatin Dynamics
- Marine Invertebrate Physiology and Ecology
- Genetic diversity and population structure
- Plant Pathogens and Resistance
- Developmental Biology and Gene Regulation
- Plant Pathogens and Fungal Diseases
- Microbial Community Ecology and Physiology
- Biofuel production and bioconversion
- Marine Sponges and Natural Products
- Enzyme-mediated dye degradation
- Microbial Metabolism and Applications
- Wastewater Treatment and Nitrogen Removal
- Marine Bivalve and Aquaculture Studies
- Bioenergy crop production and management
- Aquaculture disease management and microbiota
- Echinoderm biology and ecology
- Yeasts and Rust Fungi Studies
- Coral and Marine Ecosystems Studies
- Laser Material Processing Techniques
- Ichthyology and Marine Biology
National Nuclear Security Administration
2024
Kansas City National Security Campus
2024
Santa Cruz County Office of Education
2021
Dovetail Genomics (United States)
2016-2020
Rice University
2010-2016
Joint Genome Institute
2002-2011
University of California, Berkeley
2004-2011
Washington University in St. Louis
2011
University of Wisconsin–La Crosse
2011
Research Organization of Information and Systems
2011
The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent both an increased focus on genomics from funding agencies, application inexpensive next generation sequencing. To interact this increasing body data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for genome gene family data analysis. provides view evolutionary history every at level sequence, structure, organization, while same time providing access to...
We report the draft genome of black cottonwood tree, Populus trichocarpa . Integration shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction genome. More than 45,000 putative protein-coding genes were identified. Analysis assembled revealed a whole-genome duplication event; about 8000 pairs duplicated from that event survived in A second, older is indistinguishably coincident divergence and Arabidopsis lineages. Nucleotide substitution, tandem gene...
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such available only a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling highly accurate nearly genomes. Here we present lessons learned from generating 16 that represent six major vertebrate...
Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They responsible for ∼20% of global carbon fixation. We report the 34 million–base pair draft nuclear genome marine diatom Thalassiosira pseudonana and its 129 thousand–base plastid 44 mitochondrial genomes. Sequence optical restriction mapping revealed 24 diploid chromosomes. identified novel genes silicic acid transport formation silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes several...
The first chordates appear in the fossil record at time of Cambrian explosion, nearly 550 million years ago. modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate origins chordate and vertebrates, we generated draft protein-coding portion genome most studied ascidian, Ciona intestinalis . contains ∼16,000 genes, similar number other invertebrates, but only half that found vertebrates. Vertebrate gene families are typically simplified form ,...
The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less one-sixth sequence, gene loci occupy about one-third genome. As with human are not evenly distributed, but clustered into sparse dense regions. Some “giant” genes were observed that had average coding sequence sizes spread genomic lengths significantly larger those their orthologs....
Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, Cnidaria. Here, we report a comparative analysis of draft genome an emerging cnidarian model, starlet sea anemone Nematostella vectensis . The is complex, gene repertoire, exon-intron structure, large-scale linkage more similar to vertebrates than flies or nematodes, implying that ancestor was similarly complex. Nearly one-fifth inferred genes novelties, which...
Lancelets (‘amphioxus’) are the modern survivors of an ancient chordate lineage, with a fossil record dating back to Cambrian period. Here we describe structure and gene content highly polymorphic ∼520-megabase genome Florida lancelet Branchiostoma floridae, analyse it in context evolution. Whole-genome comparisons illuminate murky relationships among three groups (tunicates, lancelets vertebrates), allow not only reconstruction complement last common ancestor but also partial its genomic...
Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass simple sugars that are converted chemical intermediates biofuels, such as ethanol. We assembled 89 scaffolds (sets ordered oriented contigs) generate 34 Mbp nearly contiguous T. genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering utility effectiveness carbohydrate-active enzymes reesei, its encodes fewer than any other sequenced fungus able hydrolyze...
Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying evolution metazoan multicellularity, we sequenced and analysed genome unicellular choanoflagellate Monosiga brevicollis. The contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion signalling protein domains otherwise restricted to Here show physical linkages among often differ between M. brevicollis metazoans, suggesting abundant domain...
Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and sudden oak death ramorum. Oömycetes such as these species share kingdom Stramenopila with photosynthetic algae diatoms, presence of many genes probable phototroph origin supports a ancestry stramenopiles. Comparison two species' genomes reveals rapid expansion diversification protein families associated plant infection hydrolases, ABC transporters, toxins, proteinase inhibitors, and, in particular,...
Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence Amphimedon queenslandica, a demosponge Great Barrier Reef, and show it is remarkably similar to animal genomes in content, structure organization. Comparative analysis enabled by sequencing sponge reveals genomic events linked origin early evolution animals, including appearance, expansion diversification pan-metazoan transcription factor,...
To explore the origins and consequences of tetraploidy in African clawed frog, we sequenced Xenopus laevis genome compared it to related diploid X. tropicalis genome. We characterize allotetraploid origin by partitioning its into two homoeologous subgenomes, marked distinct families 'fossil' transposable elements. On basis activity these elements age hundreds unitary pseudogenes, estimate that progenitor species diverged around 34 million years ago (Ma) combined form an 17–18 Ma. More than...
White rot fungi efficiently degrade lignin, a complex aromatic polymer in wood that is among the most abundant natural materials on earth. These use extracellular oxidative enzymes are also able to transform related compounds found explosive contaminants, pesticides and toxic waste. We have sequenced 30-million base-pair genome of Phanerochaete chrysosporium strain RP78 using whole shotgun approach. The P. reveals an impressive array genes encoding secreted oxidases, peroxidases hydrolytic...
As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report sequencing and analysis of ∼98 million base pair nuclear genome placozoan Trichoplax adhaerens. Whole-genome phylogenetic suggests that belong to ‘eumetazoan’ clade includes cnidarians bilaterians, with sponges as earliest diverging animals. The compact shows conserved gene content, structure synteny in relation human other complex...
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation DNA chromatin living tissue can address this problem, dramatically increasing scaffold contiguity assemblies. Here, we describe a simpler approach (“Chicago”) based on vitro reconstituted chromatin. We two Chicago sets with human developed statistical model new software pipeline (“HiRise”) identify...
Hydra, first described by Anton van Leeuwenhoek in a letter to the Royal Society 1702, has been studied biologists for centuries and now is an important model work on axial patterning, stem cell biology regeneration. Its genome, over half of which made up mobile elements, sequenced, as genome Curvibacter sp. bacterium stably associated with Hydra magnipapillata. Comparisons those other animals provide insights into evolution epithelia, contractile tissues, developmentally regulated...
The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African laevis with more tractable genetics. Here we present a draft genome sequence assembly X. tropicalis. This encodes than 20,000 protein-coding genes, including orthologs at least 1700 human disease genes. Over 1 million expressed tags validated annotation. More one-third consists transposable elements, unusually prevalent DNA transposons. Like other...
Microbial methane consumption in anoxic sediments significantly impacts the global environment by reducing flux of greenhouse gases from ocean to atmosphere. Despite its significance, biological mechanisms controlling anaerobic oxidation are not well characterized. One current model suggests that relatives methane-producing Archaea developed capacity reverse methanogenesis and thereby consume produce cellular carbon energy. We report here a test "reverse-methanogenesis" hypothesis genomic...
The Base of the Animal Tree? identity most basal lineages animal kingdom evolutionary tree has long been contested. Ryan et al. (p. 10.1126/science.1242592 ; see Perspective by Rokas ) sequenced genome ctenophore warty comb jelly or sea walnut, Mnemiopsis leidyi , and conclude that ctenophores alone, not sponges clade consisting both cnidarians, are extant animals. results suggest a specific process likely occurred—including repeated gains loss mesoderm, expansion genes associated with cell...
Comparative analysis of the genomes one mollusc (Lottia gigantea) and two annelids (Capitella teleta Helobdella robusta) enable a more complete reconstruction genomic features last common ancestors protostomes, bilaterians metazoans; against this conserved background they provide first glimpse into lineage-specific evolution diversity lophotrochozoans. This paper presents draft genome sequences — freshwater leech (Helobdella bristly, segmented marine worm teleta) mollusc, owl limpet...
The smallest known eukaryotes, at ≈1-μm diameter, are Ostreococcus tauri and related species of marine phytoplankton. genome lucimarinus has been completed compared with that O. . This comparison reveals surprising differences across orthologous chromosomes in the two from highly syntenic most cases to almost no similarity. Species divergence these phytoplankton is occurring through multiple mechanisms acting differently on different likely including acquisition new genes horizontal gene...
Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution the origin vertebrates, we intensively searched for particular genes, gene families, conserved noncoding elements in sequenced genome cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox opsin genes involved neural crest development, nuclear receptor encoding components...
Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes, ocean waters. To further describe the cosmopolitan nonthermophilic Crenarchaeota, we analyzed genome sequence one representative, uncultivated sponge symbiont Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting same host partitioned into two dominant populations, corresponding to previously described a- b-type ribosomal RNA variants. Although they were syntenic, overlapping ribotype genomes...