DOE JGI researchers describe the current challenges in single-cell genomics. The Science: DOE JGI researchers review the status of single-cell genomics, and how close scientists are to being able to reconstruct an individual cell’s genome. The Impact: As an alternative method of studying microbial communities, single-cell genomics allows researchers to link function to phylogeny without… [Read More]

DOE JGI, JBEI researchers collaborate on improving terpene production in E. coli. Science: Researchers from the DOE JGI and the Joint Bioenergy Institute identified genes in an E. coli microbial metabolism pathway that could improve the production of terpenes. The Impact: Terpenes are high-energy compounds produced in microbes and plants that could be used for… [Read More]

Unlike many other white rot fungi, P. gigantea prefers to colonize freshly-harvested wood. The Science: Researchers sequenced and analyzed the white rot fungus Phlebiopsis gigantea, which can break down fresh-cut conifer sapwood. They also sequenced and analyzed the set of P. gigantea’s secreted proteins (secretome) and the set of all of its RNA molecules (transcriptome)…. [Read More]

Genetic maps improve the reference genome assembly of the candidate bioenergy feedstock The Science: A team of French researchers developed an array that allowed them to produce high-resolution genetic maps of two eucalyptus species that they then compared to the reference genome of eucalyptus produced by a team including DOE JGI researchers. The Impact: The… [Read More]

Three publications are featured in the Special 10th Anniversary issue. The Science: To mark its 10th anniversary, the journal Nature Methods released a Special Issue highlighting impactful articles. Among these noteworthy articles are three from DOE JGI researchers. The Impact: Microbial Sequencing is one of the areas of methods development highlighted by the journal, and… [Read More]

Water availability is often a factor in how variants of plant species evolve. The Science: Researchers statistically mapped regions of the panic grass genome linked to morphological traits such as thriving under scarce (xeric) or moderate (mesic) water availability. The information lends insights into how ecotypes are formed as evolving populations of a species adapt… [Read More]

A publicly available repository allows genomics researchers to compare multiple assemblers. The Science: A repository of genome assemblers is being developed to automate the process of selecting the best assembler for the task at hand. The Impact: There are many different genome assemblers being introduced and touted. On the nucleotid.es site (http://nucleotid.es/), the test results… [Read More]

Analysis track origins of algal light sensors to a shared ancestor approximately one billion years ago. The Science: Researchers determined the origin of a group of protein-based light sensors in land plants and a series of related phytoplankton by sequencing and comparing RNA in these genomes. The Impact: Marine phytoplankton are considered responsible for roughly… [Read More]

Many unannotated genes identified through sequencing multiple lines of the model grass. The Science Researchers used deep sequencing to look at whole-genome sequence variation in seven lines of the model grass Brachypodium distachyon and found previously unannotated genes. They also looked at genome-wide gene expression under drought-stress conditions. The Impact Hundreds of genes not present… [Read More]

Metagenomics and single-cell genomics are providing the first substantial genomic data on uncultured microbes in extreme environments. The Science: Genomes from novel lineages of bacteria and archaea in extreme environments have become accessible through techniques such as metagenomics and single-cell genomics. The Impact: Applying single-cell genomics and metagenomics toward uncultivated microbes in extreme environments has… [Read More]