Researchers assembled genomes from several single-cell isolates of the SAR11 group of Alphaproteobacteria and found that they form microclusters within the freshwater clade.
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…
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…
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,…
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…
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…
Fungi and plants working hand-in-hand
Genomic analysis of an ancient companion of plants shows expanded genes for phosphorus fixation and cell-to-cell communication The Science: More than two thirds of the world’s plants depend on arbuscular mycorrhizal fungi (AMF, also called glomeromycota) because of their ability to fix phosphorus. By analyzing the genome of one AMF, Rhizophagus irregularis (formerly Glomus intraradices),…
An insider’s view of bacterial assembly line
A combination of time-lapse fluorescence and transmission electron microscopy reveals how cyanobacteria put together an essential component The Science Cyanobacteria use carboxysomes to make their own energy by “fixing” carbon from carbon dioxide from ocean waters and other aquatic and terrestrial habitats. After deleting the genes cyanobacteria need to build carboxysomes, researchers introduced fluorescent-tagged components…
Mary Ann Moran, University of Georgia
Distinguished Research Professor, Department of Marine Sciences, University of Georgia Collaborated with JGI since 2007 We have been working with JGI on metatranscriptomic studies, using gene expression data to link activity, taxonomy, and function within marine microbial communities; and on model organism studies of bacteria-phytoplankton interactions in the ocean. The goal of our research is to identify…
Jeff Dangl, University of North Carolina
Howard Hughes Medical Institute (HHMI) investigator, University of North Carolina, John N. Couch Professor of Biology Collaborated with JGI since 2008 My lab has been engaged with JGI on a long-range project looking at the complex network of life of the microbiome that inhabits the rhizosphere and endosphere —the niches immediately surrounding and inside a plant’s root. Science…