Preparing for a Sequence Data Deluge

Accepted 2019 JGI Community Science Program proposals requested terabases of sequence data.

Over the summer, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, set an “institutional best” record by sequencing 20.4 trillion bases (Terabases or Tb) in a single month in Walnut Creek, Calif. Given the scale of sequence generation possible, the annual call for JGI Community Science Program (CSP) proposals included a cap of 2.5 Tb of sequence data per proposal, though collaborative proposals could request as much as 40 Tb, and the submissions scaled up accordingly.

“These new CSP projects not only expand on and improve our collection of reference genomes, but deeply explore the structure and regulation of their genes,” said Susannah Tringe, JGI User Programs Deputy. “They leverage new capabilities and higher throughput in DNA sequencing, synthesis and metabolomics to advance DOE mission science.”

The 23 approved CSP 2019 proposals were selected from 84 full submissions based on 105 letters of intent. Click here to see the full list of approved CSP 2019 proposals. Additionally, just over half of the accepted proposals come from primary investigators who have never led any previously accepted JGI proposal.

Among this year’s accepted proposals:

• Sugarcane very efficiently converts solar energy into plant biomass, and produces 80 percent of the world’s sugar. Following on the 2017 approved proposal to produce a first draft of a sugarcane genome sequence, Angelique D’hont of the French research institute CIRAD aims to sequence accessions representative of the Saccharum genus and key sugarcane cultivars for sugarcane diversity.
• While hundreds of high-quality fungal draft genomes have been assembled, many by the JGI, Michael Freitag of Oregon State University contends that’s not enough. He asks that 25 fungal genomes, selected from across the kingdom and already having large “genome-wide” datasets, many generated by JGI, be completed “telomere-to-telomere” and validated. “The next quantum leap in biology will come from integrating all levels of genome, transcriptome, proteome, and metabolome data into databases that allow visualization and detailed cross-species comparisons,” he wrote in his proposal. “For this, the foundation, namely the complete genomes and genome annotations, must be sound. Otherwise we will build edifices on sand instead of solid ground.”
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  At a field site in Australia where Hui-ling Liao is studying the relationship between mycorrhizal fungi and exotic pines, an Amanita muscaria was spotted fruiting beside the team’s soil core. (Sunny Liao)

  At the 2017 JGI Genomics of Energy & Environment Meeting, University of Wisconsin-Madison microbial ecologist Trina McMahon made the case for conducting long-term time series studies (watch her talk at bit.ly/JGI2017TMcMahon). Her proposal calls for sequencing up to 1,000 metagenomes from samples collected over nearly 20 years in two freshwater lakes to understand how microbial communities in these waters change in composition, function and diversity. The proposal makes use of the JGI’s very high sequencing throughput, enabled by the Illumina NovaSeq. The lakes from which the samples were collected are part of the North Temperate Lake Long Term Ecological Research (NTL-LTER) program funded by the National Science Foundation.

• To better understand how fungi orchestrate gene expression in response to key environmental conditions and vital substrates, Laszlo Nagy of Hungary’s Biological Research Center, along with 39 collaborators around the globe, plans to generate broad comparative epigenomic data sets for five widely used fungal model organisms (Anaeromyces robustus, Neurospora crassa OR74A, Coprinopsis cinerea AmutBmut, Aspergillus niger N402, and Phanerochaete chrysosporium RP78).
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  Morphological diversity of Sordariales growing in the lab. Pierre Gladieux’s proposal explores functional diversity in Neurospora and its relatives. (Pierre Gladieux, INRA Montpellier)

  Seagrasses store huge amounts of carbon, and the global loss of seagrass due to direct human activities is estimated at nearly a third of the total area, which has a significant influence on the global carbon cycle. In 2016, JGI reported the first seagrass genome, Zostera marina. Yves Van de Peer of Belgium’s Ghent University aims to build upon that effort with the Marine Angiosperm Genome Initiative (MAGI) to sequence and annotate five seagrass genomes. (Watch Jeanine Olsen’s talk on Zostera marina from the 2016 JGI Genomics of Energy & Environment Meeting at bit.ly/JGI2016Olsen.)

• More than a decade ago, JGI launched the first effort toward developing the Genomic Encyclopedia of Bacteria and Archaea (GEBA). By 2017, the genomes of more than 1,000 phylogenetically diverse bacteria and archaea had been sequenced by the JGI. The latest GEBA proposal, led by William Whitman of Georgia Tech, is the largest project to date, with a goal of sequencing 10,000 microbes, half of them type strains, and coupling the sequences with transcriptomics and metabolomics. “This is an excellent showcase of how JGI is bringing together the community to push the borders of science,” said Prokaryote Super Program head Nikos Kyrpides.

Aside from the sheer scale and scope, several of the 23 accepted proposals included plans to analyze and distribute data and results through the DOE Systems Biology Knowledgebase (KBase), soon to be co-located with the JGI in the Integrative Genomics Building at Lawrence Berkeley National Laboratory. The data generated from these proposals will enable multiple research communities to tackle questions of relevance to DOE missions in energy security and sustainability and global biogeochemistry.