DOE Joint Genome Institute

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Regulatory Genomics of Brachypodium

This is a proposal to develop the most advanced systems-level understanding of transcriptional regulation of grass growth. Brachypodium distachyon is a model system for the study of energy crops such as sorghum, miscanthus, and switchgrass, and the team’s approach depends on a unique combination of reagents that were developed in collaboration with JGI. The identification… [Read More]

Fungal Comparative ENCODE Project

The FUNCODE project aims to generate a genome-wide library of the rules that govern gene expression in five important model fungi. The resources generated during the project will support a wide range of basic and applied research and biotechnological and industrial applications of fungi, including an understanding of gene regulatory circuits behind plant waste decomposition… [Read More]

Genome Encyclopedia of Bacteria and Archaea VI

The proposed study will advance the sequencing of the type strains of prokaryotes and initiate the functional genomics of understudied groups. The goal of these studies is to improve our understanding of gene function for a wide variety of prokaryotes. Ultimately, a predictive model of prokaryotic life on earth will be developed to unite gene… [Read More]

Short-Term Temperature Shift at Harvard Forest

Long-term warming results in significant changes in respiration, community structure and microbial processes. The primary goal of this project is to separate molecular changes resulting from long-term warming from temperature effects of gene expression using samples just prior to the power returning and the week afterwards when the soil temperature is again 5°C higher than… [Read More]

From Genome to Watershed Scales

The quality of water that leaves the watershed is impacted by soil microbial communities that will be studied here. The research will target regions along the East River, a tributary of the Colorado River, focusing on three subsystems: the river corridor and hillslopes and consider effects of time of year, depth below the surface and… [Read More]

Microbial Functions at Soil-Aquatic Interfaces

47-55 percent of the terrestrial carbon is transported and processed in rivers. Terrestrial carbon is generally considered to be resistant to aquatic microbial metabolism. However, recent evidence suggests that at soil-aquatic interfaces terrestrial carbon can be respired by aquatic microorganism at the cost of low carbon use efficiency thus contributing to CO2-fluxes to the atmosphere…. [Read More]

DNA Methylation Role in Basal Fungi

DNA methylation is a fundamental epigenetic modification that plays a critical role in genome function in eukaryotes. This proposal will study the function of N6-methyladenine (6mA) in early divergent fungi because it is more abundant than in other eukaryotes and seems to regulate gene expression. The function will be studied in the context of responses… [Read More]

Fungal Gene Expression for Biomass Conversion

The filamentous fungus Neurospora crassa is an important model organism for fungal conversion of biomass. It is unknown how DNA structure is altered in response to stimuli to change expression levels of genes involved in biomass conversion. The goal is to define the global regulatory network of DNA structures in N. crassa and its impact… [Read More]

Comparative Genomics of Acutodesmus

Green algae are important contributors to global carbon cycling and hold great promise as feedstocks for biomass and biotechnology applications. To date, breeding and natural variation of green algae have not been exploited for strain improvement due to lack of foundational knowledge about strain diversity and sexual cycles. This project will investigate natural strain diversity,… [Read More]

Reference Genomes for 50 Rust Fungi

Rust fungi are the largest group of plant pathogens. Different species cause disease on important food, timber and bioenergy crops. However, there are comparatively few genetic resources available for this group. The goal of the rust pangenomics project is to provide reference genomes for 50 rust species, including pathogens of JGI plant flagship species (e.g.,… [Read More]