One of the challenges in studying grasses for bioenergy applications is that they typically have long lifecycles and complex genomes. Jeremy Schmutz, head of the DOE JGI Plant Program at the HudsonAlpha Institute of Biotechnology, pointed out that foxtail millet has several advantages as a model. It’s a compact genome roughly half a billion bases…
Relative Reference: Foxtail Millet Offers Clues for Assembling the Switchgrass Genome
Arranging DNA fragments into a genome sequence that scientists can interpret is a challenge often compared to assembling a puzzle, except there is no box to provide an idea of what the picture is even supposed to be. Sometimes there’s guidance in the form of other publicly-available DNA sequences from related organisms that can be…
Microbes as the unknown variable in thawing permafrost
Permafrost covers a quarter of the Earth’s land surface and stores significant amounts of carbon. As global temperatures rise and cause the frozen soils to thaw, so have concerns on the fate of the stored carbon and on the global climate. One of the recent studies that looked at this question was conducted by researchers…
Mount Marty College students wrap first project with DOE JGI’s “Interpret a Genome” program
“Annotating genes is a lot of work, and you have to pay a lot of attention to detail,” said April Knapp, one of seven students who presented findings from the class’s research Friday. “But it’s also very interesting because bioenergy and biofuel is such a high-needs fields. To know that the research we did here…
Overcoming short-read genome sequence assembly challenges
The genome assembly challenges posed by short sequence reads from sequencing platforms such as 454/Roche and Illumina are well-documented; the lack of reference genome data can hinder attempts to put together the myriad of short DNA sequences. Researchers from the Georgia Institute of Technology and the DOE JGI wanted to determine the impact of short…
An alternative surrogate for gene discovery in switchgrass
Selected for the DOE JGI 2007 Community Sequencing Program because of traits such as high yield, perennial growth and low nutrient requirements, switchgrass is a promising candidate bioenergy crop that could be used to develop cellulosic biofuels. One of the challenges with sequencing switchgrass is the fact that it is a polyploid, containing multiple, full…
Effects of symbiosis on a fungal transcriptome
The soils of the boreal forests in the northern latitudes are estimated to store more than three times the amount of carbon contained in the atmosphere or in plant life on land. Recent studies suggest the relationship between fungi on the forest floor, plants and the microbial communities at the plant roots (or rhizosphere) plays…
Analysis of a TCE-degrading metagenome
Groundwater sites contaminated with compounds such as trichloroethene (TCE), a pervasive organic groundwater pollutant often used by industry as cleansers or degreasers.Dehalococcoidesbacteria, often found in a community of other microorganisms at groundwater sites contaminated with these compounds, can break down TCE and convert it into ethene, a harmless chemical compound often used to help ripen…
White rot fungal genomics analysis on EcoSeed
Scientists at the Energy Department’s Joint Genome Institute are comparing the genetic structure of two strains of white rot fungi in order to develop better enzymes for biofuel production.White rot fungi digest moist wood, causing it to rot and decay. These fungi possess natural enzymes that break down the cellulose, hemicelluloses and lignin of plant…
Searching for the basis of ligninolytic selectivity
Many fungal genome projects being carried out at the DOE JGI focus on understanding how enzymes can break down cellulose and lignin, the two most abundant biopolymers on Earth, in order to harness these capabilities for industrial applications such as biofuels production. Scanning electron micrograph of Ceriporiopsissubvermispora mycelium on wood. (Robert Blanchette, University of Minnesota)…