Community-driven CAMI Challenge offers analysts, scientists insights on the right tools for their research questions. They are everywhere, but invisible to the naked eye. Microbes are the unseen, influential forces behind the regulation of key environmental processes such as the carbon cycle, yet most of them remain unknown. For more than a decade, the U.S….
2018 DOE JGI Community Science Program Allocations Announced
Proposals encompass multiple capabilities of the national user facility Though organisms can be studied in isolation, a more comprehensive picture emerges when their environmental interactions are taken into account. Along the same lines, many of the 30 proposals selected for the 2018 Community Science Program (CSP) of the U.S. Department of Energy Joint Genome Institute (DOE…
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…
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….
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…
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…
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,…
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.,…
Comparative and Population Genomics of Xylariaceae
Despite evidence that endophytes play a critical role in plant-microbe interactions, they are poorly represented in genome databases. Leveraging our unique culture collection, the team proposes a genomic survey of the Xylariaceae, one of the largest and most diverse families of fungi made up of endophytic, pathogenic, and saprotrophic (including wood degrading) species. Our project…
Open Green Genomes Initiative
The Open Green Genomes Initiative will generate high-quality genome assemblies and annotations for 35 species representing all major evolutionary lineages in the land plant tree of life. This work will greatly improve comparative analyses of the genes, regulatory networks and metabolic pathways influencing plant growth, responses to environmental stress, and production of valuable plant products….