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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Home › Items tagged with: 454 sequencing

Content Tagged "454 sequencing"

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November 8, 2011

DOE JGI sequencing capabilities in InSequence

The US Department of Energy’s Joint Genome Institute is tweaking its sequencing technology lineup as it gears up to produce more than 47 trillion bases of DNA sequence in the 2012 fiscal year, with more than half that sequencing output slated to go toward its largest user program, the Community Sequencing Program. Read more on GenomeWeb [Read More]

January 21, 2011

Citrus genomes project on PharmPro

Researchers from the International Citrus Genomics Consortium announced this weekend at the Plant and Animal Genome (PAG) XIX conference in San Diego, California the availability of the sequence  assembly and annotation of the first citrus genomes, the sweet orange (Citrus sinensis) and the Clementine mandarin (Citrus clementina). The sweet orange genome was sequenced and analyzed… [Read More]

January 21, 2011

JGI Highlight: More Caldicellulosiruptor bacterial genome sequences

The Caldocellulosiruptor genus contain bacteria that are capable of producing hydrogen and degrading plant biomass. Found all over the world, such as in geothermal hot springs in Russia and Iceland to solar-heated mud flats in California, the bacteria thrive in high temperatures. C. saccharolyticus (Image courtesy of A. Pereira & M. Verhaart, Wageningen University, Netherlands)… [Read More]

January 18, 2011

Citrus Genomes project on StreetInsider.com

“The immediate availability of these annotated assemblies will enable breeders to mine the database for genes associated with key agricultural traits, such as disease-resistance, temperature tolerance, fruit quality, and yield,” explained Fred Gmitter, Chair of the International Citrus Genomics Consortium and a citrus geneticist and breeder at the University of Florida. “In addition, they will… [Read More]

January 18, 2011

Citrus Genomes project on PR-Inside

Funded in part by the Florida Citrus Production Research Advisory Council, a citrus grower industry organization, the project is expected to assist geneticists and breeders improve these important fruit crops. The assembled and annotated genomes have been added to the publicly available database Phytozome.net, a project of the DOE JGI and the Center for Integrative… [Read More]

January 18, 2011

Citrus Genomes project on TMCnet.com

The sweet orange joins the growing list of plant genomes sequenced using next-generation 454 Sequencing Systems. Throughout just the last year, international research teams announced the draft sequences of the apple, cassava, soybean, wheat, wild strawberry, and cacao genomes, representing some of the most economically important crops for global food supply. Read more on TMCnet.com. [Read More]

January 18, 2011

Citrus Genomes Announcement on Enhanced Online News

Researchers from the International Citrus Genomics Consortium announced this weekend at the Plant and Animal Genome (PAG) XIX conference in San Diego, California the availability of the sequence assembly and annotation of the first citrus genomes, the sweet orange (Citrus sinensis) and the Clementine mandarin (Citrus clementina). The sweet orange genome was sequenced and analyzed… [Read More]

January 17, 2011

Citrus Genome Sequences on GenomeWeb Daily News

For the sweet orange sequencing project, which was spearheaded by researchers at the US Department of Energy’s Joint Genome Institute, the University of Florida, the Georgia Institute of Technology, and 454 Life Sciences, the team used the Roche 454 GS FLX and FLX Titanium platforms to tackle the 320 million base genome of the Ridge… [Read More]

October 18, 2010

JGI sequencers on GenomeWeb

The US Department of Energy Joint Genome Institute now uses a collection of next-gen sequencers from a variety of firms, following the phasing out of its Sanger machines. Read more on GenomeWeb. [Read More]

November 20, 2009

DOE JGI early tester of 454’s benchtop sequencer on Y!Finance

454 Life Sciences, a Roche Company (SWX:RO) (SWX:ROG), announced today at the Association of Molecular Pathology Annual Meeting in Kissimmee, Florida a series of revolutionary developments which significantly expand the company’s high-throughput sequencing portfolio. Addressing the growing demand for next-generation sequencing data in everyday biological and clinical research, the company revealed the new GS Junior… [Read More]
Page 1 of 212»

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