Accepted proposals emphasize JGI interests in algae and secondary metabolites.
Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
A total of 27 proposals have been approved through the annual Community Science Program (CSP) call of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab). The accepted proposals come from 80 full proposals, resulting from 95 letters of intent. For the first time, 63 percent of the accepted proposals come from investigators who have not previously been a principal investigator (PI) on an approved JGI proposal.
Approved proposals make use of JGI’s breadth of capabilities while also highlighting collaborative research of a scale exceeding a single lab’s capacity. Additionally, the call recommended including plans to analyze and distribute data through the DOE Systems Knowledgebase (KBase), a free, open source data science platform that allows users to explore data and share reproducible analyses with collaborators and the broader community.
High oleic pennycress. (Courtesy of Ratan Chopra)
The approved proposal from Alex Harkess of Auburn University started as a small-scale white paper focused on duckweed through the CSP New Investigator call. It is the first project to have successfully evolved into a full-scale proposal known as the Brassicales Genome Initiative. Brassicales is represented by more than 4,700 species, and the proposal focuses on investigating the repeated evolution of three traits relevant to DOE interests: photosynthetic transitions, specialized metabolites, and woodiness.
A proposal from Ben Shen of The Scripps Research Institute (TSRI) launches a collaborative effort between JGI, TSRI and the University of Minnesota to establish the Natural Products Genomics Resource Center. To help enable the discovery of secondary metabolites, also referred to as natural products, the proposal includes plans to sequence several thousand Actinobacteria strains and then use computational tools to analyze biosynthetic gene clusters and then develop them for a range of applications. (Hear Ben Shen here in the JGI Natural Prodcast podcast.)
Red algal life at the extremes. Left: Cyanidiophyceae thriving in hot springs at Yellowstone National Park at Yellowstone National Park. Right: Rock-dwelling Galdeiereia phelgrea (green band in image) growing near Yellowstone hot springs. (D. Bhattacharya)
Several accepted proposals reflect JGI’s interest in algal research for bioenergy production and algae’s roles in nutrient cycling, now a facet of the Fungal & Algal Program. For example, green algae represent the largest group of primary producers generating organic compounds through photosynthesis, but only a fraction have been sequenced. Adriana Lopes dos Santos from Singapore’s Nanyang Technological University aims to generate genome sequences from underrepresented green algae groups in a wide range of environments. A similar proposal focused on diatom genomes from Thomas Mock of the University of East Anglia was also approved to learn more about the roles of diatoms in carbon fixation and in aquatic food webs. Finally, Debashish Bhattacharya of Rutgers University is interested in understanding how unicellular red algae (Cyanidiophyceae) have adapted thrive in environments including hot springs and acid mining sites, traits that might have biotechnological applications.
Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
Among the other accepted proposals:
- Amanda Hurley and Jo Handelsman of the Wisconsin Institute for Discovery (WID) are interested in sequencing secondary metabolite-producing environmental bacteria from the Tiny Earth collection. The work builds upon a pilot project to sequence antimicrobial-producing strains. Established by Handelsman, Tiny Earth aims to crowdsource antimicrobial discovery for the control of plant pathogens, partnering with 600 instructors worldwide who work with more than 10,000 undergraduate students each year.
- Brian Looney of Duke University is interested in understanding which species of mycorrhizal fungi are important for poplar plant health, in part to learn how these species can modulate their behavior in the presence of other fungi. Poplar is a JGI Flagship Plant, of interest as a candidate bioenergy feedstock.
- John McKay of Colorado State University is interested in developing mutant populations of the bioenergy feedstock crop Camelina sativa, and generating their genome sequences to improve breeding by genetic improvements.
- Apomixis is asexual reproduction through seeds, and Peggy Ozias-Akins from the University of Georgia is interested sequencing relatives of switchgrass that are apomictic. This trait would be beneficial for reproduction of improved heterozygous clones through seed.
- Eric Wommack of the University of Delaware is interested in learning how environmental conditions influence viral-host interactions in three groups: cyanophages, bacteriophages, and giant algal viruses.
Hot spring in Yellowstone National Parks’ Artist Paint Pot area. (Courtesy of Roland Hatzenpichler)
The approved proposals started October 1, 2020 and the full list is available here. They are expected to generate publicly available data relevant to DOE interests in finding solutions to energy and environmental challenges, and be of use to the larger research community.