This project aims to produce the first genome assembly of a cultivated sugarcane plant. To date no Saccharum species have been sequenced due to their large complex  polyploid genomes.  Cultivated sugarcane is grown throughout the tropics and sub tropic regions of the world and it produces 80% of the world’s sugar. Sugarcane is a C4 plant… [Read More]

This project aims to define gene function in rumen microbes to improve our knowledge of carbon (C) flow in the rumen, including the breakdown of lignocellulose, through the metabolism of substrates to volatile fatty acids (VFAs) and fermentation end products, to the final step of methane (CH4) formation. The project builds on the datasets and… [Read More]

This project would increase the sequence depth across a broader phylogenetic diversity of gymnosperms compared to previous focus on the Pinaceae. The specific transcriptomes and the genome targeted in this project would greatly accelerate our understanding of the functional and structural genomic underpinnings of the diverse secondary metabolic biosynthetic systems of these conifers, and facilitate… [Read More]

Bacteria and fungi that are intimately associated with plants comprise the plant microbiome . Interest in the role of these organisms in plant health and defense grows as research reveals the importance in modulating responses to defense and abiotic stress. Determining key and conserved nodes within the gene networks underlying these effects in a diverse… [Read More]

We will dissect the effects of fungi on post-fire soil carbon dynamics by using a systems biology approach that couples small experimental “pyrocosms”, genomics, amplicon metagenomics, transcriptomics, metatranscriptomics, and mass spectrometry. Proposer: Thomas Bruns, University of California, Berkeley [Read More]

The work continues and expands a previous effort carried out in collaboration with JGI. In the new efforts, we are taking both old and new populations through a total of at least 60 cycles of irradiation and outgrowth to achieve a level of radiation resistance that is the same or greater than that observed in… [Read More]

Here we propose to expand the search for new lineages of methanotrophs and methanogens by conducting multi-omic (DNA and RNA) sequencing in methane-rich environments enriched in uncultivated microbial “dark matter” (MDM). Specifically, we will focus on: 1) the distribution of methane metabolism in microbial dark matter; 2) capacity for facultative respiration in methanogenic archaea; 3)… [Read More]

Woody biomass makes up the major portion of terrestrial carbon, and forest ecosystems contain enormous reservoirs of lignocellulose belowground, in dead trees, and litter. Decomposition of this recalcitrant material and mobilization of nutrients are major components of the carbon cycle and essential for forest health. Whether releasing carbon dioxide (CO2) or transforming humic substances, the… [Read More]

The goal is to establish the common or crystalline ice plant (Mesembryanthemum crystallinum L.) as a DOE Plant Flagship Genome species. The ice plant was the first reported halophytic, facultative crassulacean acid metabolism (CAM) species, meaning that the plant can be induced to switch from C3 photosynthesis to CAM following water-deficit or salinity stress treatment…. [Read More]

We propose a series of comparative genomic analyses with the broad aim of identifying transcripts and putative regulatory control elements (conserved non-coding sequences; CNS) that are associated with the evolutionary transition between annual and perennial life history strategies. We will accomplish this via de novo sequencing of additional perennial Brachypodium species and a new outgroup… [Read More]