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JGI at PAG XXIV

JGI will be sharing a booth (#202) at The Plant and Animal Genome XXIV Conference (PAG) in San Diego from Sunday, January 10 through Tuesday, January 12, 2016 with our colleagues from KBase: The Department of Energy Systems Biology Knowledgebase. Also, on Tuesday, January 12, 2016 from 4:00-6:10 pm in the San Diego Room, join us… [Read More]

A cool glass of clean drinking water

A new system called ScanDrop could revolutionize how we identify pathogens in drinking water. The Science: Researchers from Lawrence Berkeley National Laboratory (the Joint BioEnergy Institute and the DOE Joint Genome Institute) and Northeastern University and the Massachusetts General Hospital/Harvard Medical School) have developed a portable, network-enabled system for testing drinking water contamination. The system, called ScanDrop, developed by… [Read More]

Ocean sponge-dwelling bacteria have hidden talents

Ocean sponge-dwelling bacteria have hidden talents. The kidney-red coral reef sponge, Theonella swinhoei, is a source of several anti-fungal and anti-cancer drug candidates. These compounds aren’t produced by the sponge itself, but by symbiotic bacteria that live inside it. The compounds in question are called polyketides, secondary metabolites that happen to be made by just two… [Read More]

Faster, bigger, stronger: improvements to two of JGI’s genome databases

Capacities for DOE JGI’s twin genome analysis systems, IMG and IMG/M have both been expanded in the last two years. The Science: The DOE Joint Genome Institute maintains the Integrated Microbial Genomes (IMG) data warehouse, which contains a rich collection of genomes from all three domains of life. IMG/M provides a similar collection of microbial… [Read More]

ENVO brings structure to biological “environments”

New tool aims to help life science researchers formalize naming conventions for the environments they study. The Science: Biological and biomedical research is increasingly referencing and compiling data from environmental samples, leading to a growing need for a formal and standardized approach to describing those environments. The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open-access… [Read More]

Out with the old, in with the new, improved Genome Portal

The newest iteration of the DOE Joint Genome Institute’s and analytical tools sports improved user interface and infrastructure. The Science: The DOE Joint Genome Institute’s massive genomic database and data management system, the Genome Portal (http://genome.jgi.doe.gov), has recently been upgraded with a more robust infrastructure to manage the torrent of genomic data available and a… [Read More]

Surprising finds in a rare plant’s mitochondrial genome

Rare and ancient plant gobbles up entire mitochondria from other plants and holds onto them for eons. The Science: One of the oldest flowering plants, Amborella trichopoda, split off from the lineage of other flower plants about 200 million years ago. Analysis reveals that it has a record-setting amount of foreign DNA in its mitochondria,… [Read More]

A gluttonous plant reveals how its cellular power plant devours foreign DNA

Amborella trichopoda, a sprawling shrub that grows on just a single island in the remote South Pacific, is the only plant in its family and genus. It is also one of the oldest flowering plants, having branched off from others about 200 million years ago. Now, researchers from Indiana University, with the U.S. Department of… [Read More]

One big family: Understanding the Polyporales phylogenetic and phylogenomic trees

Looking at a combination of whole genomes and gene databases suggests a new way to examine this fungus family tree. The Science: Researchers reviewed 10 currently available whole genomes, comparing them to known gene datasets. They reported family trees for several taxonomic subgroupings called clades. They also analyzed several single-copy genes to assess them for… [Read More]