DOE Joint Genome Institute

Our Projects
Home › CSP Plans

Finishing Genomes to Leverage Additional Information

Genomes of important model and many industrially important fungi are still incomplete. The goals of this project are: (a) to finish and annotate the genomes of ~25 strains; and, (b) to carry out functional analyses by novel CRISPR/Cas9 approaches. The next quantum leap in biology will come by integrating all levels of genome, transcriptome, proteome,… [Read More]

Insights into Functional Diversity in Neurospora

This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi. The proposal fits into the DOE mission because it focuses on biological processes of industrial interest, it explores the functional diversity… [Read More]

Marine Angiosperm Genome Initiative

Seagrasses are the only flowering plants that live in the sea. Understanding the genomic basis for their many unique adaptations is fundamental to successful management, as seagrasses are being lost globally. Seagrasses are among the world’s largest carbon sinks and thus relevant to the DOE missions carbon cycling, biogeochemistry and JGI plant flagship genomics. Translational… [Read More]

Sphagnum Microbiome Genetic Interactions

The importance of plant-microbiome systems on carbon and nitrogen processes is perhaps most pronounced in Sphagnum moss dominated ecosystems, which occupy 3% of the Earth’s land surface yet store approximately 25% of terrestrial carbon. Much of the nitrogen needed to support Sphagnum comes from a symbiosis with microbes, yet we don’t know how the symbiosis… [Read More]

Microbial Methane Production in Freshwater Wetlands

Increasing atmospheric concentrations of greenhouse gasses like methane are altering the global climate, causing catastrophic wildfires, storm events, and drought. This proposal targets microbial methane production in freshwater wetland soils, as this production is the largest natural source of methane. Results from this proposal can improve greenhouse gas predictions across the globe. Additionally, this research… [Read More]

Genome Level Diversity in Brassica rapa

To avoid competing with land use for food crops, biofuel crops are often grown on marginal land. Understanding how to improve soil health and provide enhance stress tolerance traits is essential for improving biofuel production. This study aims to explore the genome level diversity that exists in the important crop model Brassica rapa, a relative… [Read More]

Roles of Microbial Communities in the Atacama Desert

The hyperarid core of the Atacama Desert (Chile) is one of the driest deserts on Earth. Its soils represent one of the few environment types that yet have barely been investigated at the level of metagenomics. Due to the extremely low content of biomass these Atacama Desert sediments have been claimed to be Mars-like. We… [Read More]

Exploring Seaweed Genome Diversity

Seaweed represent a 6 billion dollar industry across the world, and are a source of many materials spanning the chemical and food sectors. Understanding how seaweeds construct these molecules will allow us to harness their biosynthetic machinery in the biomanufacturing of fuels, lubricants, polymers, and other commodity and specialty chemicals. To help us understand the… [Read More]

Infections and Host-Pathogen Interactions of Chlorella

The non-photosynthetic, predatory cyanobacterium Vampirovibrio chlorellavorus (Melainabacteria) is a globally important obligate pathogen of Chlorella species/strains of interest as biofuel feedstocks. This project proposes two sequencing approaches to generate information for querying: (i) pathogen and host genomics; and, (ii) the mode of infection and host reaction to infection via transcriptomics); and, (iii) explore evolution and… [Read More]

Nitrate in Coastal Waters

The proposal calls for metagenomic and metatranscriptomics sequencing, and metabolomics analysis from salt marsh sediments exposed to a decade of chronic anthropogenic nitrate enrichment. These sediments are part of a multi-PI research project at the Plum Island LTER where the team has been fertilizing two whole salt marsh creeks since 2004, while maintaining two additional… [Read More]