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2019 JGI Meeting ...... 2-3

NeLLi Symposium Highlights. . 4-5

Science Highlights...... 6-7

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Dimensions of Omics Diversity Study senior author Diane Dickel in her lab. (Thor Swift/Berkeley Lab) Notes from the 2019 JGI Technique for Studying Gene Expression Meeting Takes Root in Plants Natural Selection in

Excerpted from the Berkeley Lab release by Aliyah Kovner Kicking off the 14th Annual JGI Genomics of Energy & Environment Lawrence Berkeley National a toehold into its function. In our Meeting in San Francisco, Calif., Laboratory (Berkeley Lab) research- study, we showed that Drop-seq can Michael D. Purugganan, Dean of ers, including scientists at the U.S. help us do this.” Science at , Department of Energy (DOE) Joint Dickel has been using Drop-seq focused on two projects to better Genome Institute (JGI), a DOE Office on animal cells for several years. An understand how selection acts on of Science User Facility, have immediate fan of the platform’s ease the rice genome. successfully used an open-source of use and efficacy, she soon began One project involves developing RNA analysis platform on plant cells speaking to her colleagues working a rice fitness consequence map to for the first time. The technology, on plants about trying to use it on help crop breeders looking for called Drop-seq, allows scientists to plant cells. regions with mutations and pheno- see what genes are being expressed However, some were skeptical that typic variations. It’s based on the and how this relates to the specific such a project would work as easily. INSIGHT (Inference for Natural functions of different cell types. First off, to run plant cells through Selection from Interspersed Genomi- Prior to this study, published in a single-cell RNA-seq analysis, they cally CoHerent elemenTs) method Cell Reports, Drop-seq had only must be protoplasted — meaning developed for human genome been used in animal cells. they must be stripped of their cell studies. The greenINSIGHT method “For many of the genes in plants, walls using unique cocktails of Puruggunan’s lab developed over we have little to no understanding enzymes. Secondly, some plant four years calculates the fitness of what they actually do,” explained biologists have expressed concern impact of mutations that may be senior author Diane Dickel, who that cells are altered too significantly neutral, nearly neutral or advanta- studies mammalian genomics in by protoplasting to provide insight geous. The method allowed the team the Lab’s Biosciences Area. “But into normal functioning. And finally, to identify the rare gene variants and by knowing exactly what cell type or some plant cells are simply too big map them back to the genome. The developmental stage a specific gene to be put through existing single-cell Rice FitCons Map is expected to be is expressed in, we can start getting RNA-seq platforms. available summer 2019. continued on page 7 continued on page 2 THE

PRIMER 2019 JGI Meeting continued from page 1

Purugganan also cited the use of study the effects of drought, using uted to microbial infections, and how rice gene expression selection to stable isotope probing to find and these understandings have been measure the contribution of the map pathways of root carbon consum- linked to terms used to describe transcription levels to fitness. This ers into the soil, and using the data illness, starting with the use of is a project he waited more than for network analyses and food web “virulent” to mean “full of poison.” a decade to execute. Partnering with modelling. The team has gone from Twenty years ago, Casadevall began the International Rice Research isotopically labelling grasses in thinking of disease as an outcome Institute in the , Purugga- greenhouse chambers to field sites at of an interaction between a pathogen nan’s team used samples from plants the Hopland Research and Extension and its host. With that definition, that were either under well-watered Center in northern California. he began trying to find a mathemati- or intermittent drought conditions. “We can’t understand any interac- cal way to track the pathogenic Among their early findings from the tions without recognizing interactions potential of microbes, including fungi. resulting dataset of more than 15,000 among soil inhabitants,” she said. The fungal kingdom, Casadevall genes: they’ve found a “drought- Most interactions studied have been reminded the audience, has more escape” gene that causes the plant in isolation, such as plants and than six million species and includes to flower early. bacteria, or bacteria and viruses, but several pathogens currently doing these studies don’t give researchers significant damage to plants, insects the full picture. “We now have the and whole ecosystems. Humans and tools that enable exploration of the mammals, he noted, are compara- complex interactions that occur in tively resistant to fungal pathogens; soil,” she added, listing an arsenal credit goes to adaptive immunity that includes omics, isotopic tools, and high body temperatures. mass spectroscopy, statistics, All of this led Casadevall back and modelling. to the question of the great lizards: “Don’t ask what killed the dinosaurs, ask ‘What kept the reptiles from having a Second Reptilian Age?’” The answer is the same as the question of why Michael Purugganan humans are here and others he raised at the beginning of his talk: fungi. Fully Understanding Soil Microbiome Interactions In her keynote address, Mary Firestone of the University of California, Berkeley, emphasized the need to Mary Firestone understand the full picture of soil microbiome interactions. The com- plexity was underscored by the plethora of research collaborations, Preventing a Second and lab members past and present Reptilian Age who have helped describe the interac- In his closing keynote, Arturo tions within and across domains thus Casadevall of the Johns Hopkins Arturo Casadevall far to better understand the composi- School of Public Health led with the tion and function of soil microbiomes. human existential questions, “Why Firestone’s long-term goal is to are we here?” and “Why do we eat Diversity in All Dimensions learn about the interactions among so much?” to explain why dinosaurs Geri Richmond, noted chemist plants, bacteria, fungi, viruses and no longer roam the earth. at the University of Oregon and mesofauna in the soil. She talked He briefly recapped how people a strong advocate for diversity in the about work using dominant grasses have come to understand the origins scientific workforce, asked attendees in northern and southern California to of illnesses before they were attrib- to consider serving as a mentor to the

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next-generation workforce. “Good innovation and high impact research thrives on diversity in all dimensions,” she reminded them. Richmond should know; alongside her research career, she is founding director of the grass- roots organization COACh, which has helped advance the careers of thou- sands of women scientists and engineers around the world. Among her accolades are the National Medal of Science and the 2018 Priestley Medal, the American Chemical Society’s highest honor. “Social diversity causes discomfort and we have to work harder,” she acknowledged while highlighting the economic benefits of diversity, “but that brings out the creativity.” She asked attendees to consider mentor- ing, serving in the short-term either Annual JGI Meeting Poster Session as a coach who can help refine specific skills, or as a sponsor who can help advance someone’s career, the fungi need LOV — the light, logical implications of automation in or else as a long-term mentor who oxygen & voltage protein domain in biofoundries and multiomics facili- supports and encourages someone’s Neurospora crassa. ties, including the JGI. She pointed growth and development. Aesthetics aside, he added, the out that in the challenge of scaling up images produced through fungal production and reducing human error, “All You Need is LOV” bioluminescence raise several scien- researchers may not recognize that tific questions, including transcrip- they’re shifting their thinking from Some fungi can sense to environ- tional dynamics, cell-cell communica- how to conduct the experiment to how mental factors such as light and tions, and fungal adaptation to light. they can optimize and efficiently use gravity, and respond by changing their Continuing with the photography the equipment. Building a facility and growth patterns accordingly. Luis analogy, Larrondo’s team built a pin- the underlying infrastructure, she Larrondo of the Pontificia Universidad hole camera to allow the “blind” reminded the audience, is about Catolica de Chile combines synthetic Neurospora to sense light intensities. giving the team’s vision and aspira- biology and what he calls “optogenet- They did this by developing a promot- tions form, and making design ics,” how cellular processes can be er that responds to light, and then choices that reflect this goal. activities or repressed by light and combining it with Neurospora’s Frow asked attendees to consider genetics, to learn more the circadian circadian clock that controls daily the relationships between machines rhythms in fungi. rhythms in gene expression. The and humans, adding that while the Larrondo demonstrated how fungi result: an image that slowly appears human component isn’t often taken streaked on a plate can distinguish and then fades over the course of into account when developing work- light intensities. The image is a day, and then reappears following flows, somehow the information and projected onto a plate on which the the fungal cycle. skills need to be transferred. “Infra- fungi are growing. The plate acts as structure for bioengineering requires a photographic film, and after the Worldbuilding with the complex integration of mechani- fungi have genetically processed the cal, digital, biological and human light, they emit bioluminescence in Automation systems,” she concluded. “Automa- a form that replicate the image. To Emma Frow from the University of tion… is a widely accepted choice, do that, Larrondo told the audience, Arizona opted to focus on the socio- but it’s not inevitable.”

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THE PRIMER NeLLi 2019

Highlights from the New Lineages of Life Symposium

A Paradigm Shift on Eukarya

Thijs Ettema of Wageningen University opened the JGI’s NeLLi 2019 Symposium: From New Lin- eages of Life to New Functions, with the proposal that there are two domains of life — and eukarya is not one of them. Countering Carl Woese’s 40-year old argument that the Tree of Life has three domains of life, he suggested that eukaryotes evolved from a specific clade of archaea rather than being a separate branch with shared common ancestry. With this theory in mind, Ettema’s lab has been working on identifying what he called the “founding ar- chaeal lineages” of eukaryotic cells New Lineages of Life Symposium Poster Session by looking for the direct descendants of the host cell, and the mitochon- Ettema closed by recapping the Using this archaeon, Schleper and drial ancestor. In 2015, Ettema and argument that eukaryotes are chimeric her colleagues are tracking down fellow NeLLi Symposium keynote in nature, and that one of the Asgard the last common ancestor of all Christa Schleper published a paper lineages may be a sister relation of Thaumarchaeota (LACAOA), to learn on the eukaryotic nature of Asgard the ancestral eukaryote cell. more about how early life evolved. archaea (named for one of the nine And they are finding that this is worlds in Norse mythology), which Not Hot, But Lukewarm a series of successive gains rather represent the closest relatives of than a single event or leap. When eukaryotes. The Ettema lab has Archaea are thought to have analyzing the archaeal genome, they focused on Asgard archaea since originated in hot springs, and gener- found that N. cavascurensis turned out then, and through collaborations, ally considered extremophiles. In to be an ammonia-oxidizing archaea they’ve greatly increased the number her keynote, Christa Schleper of (AOA) that branches early. Additionally, of Asgard archaeal lineages. In the the University of Vienna focused on the genome contains mobile elements current pantheon of Asgard archaeal archaea that have adapted to thrive acquired through lateral gene transfer, diversity Frigga, Idunn, Frey and Hela in more moderate environments. suggesting the archaeon acquired are among those joining Odin, Thor, Thaumarchaeota are found in a wide genes that allowed it to thrive outside Loki and Heimdall. range of environments including extreme environments. oceans, soil, human skin, some wastewater treatment plants, and even ultraclean rooms in NASA. “They may already be on Enceladus,” she noted, referring to an ice-clad moon of Saturn. Searching for clues on how and why Thaumarchaeota thrives in a wide range of environments, the Schleper lab focused on a species called Nitroscocaldus cavascurensis that they Thijs Ettema isolated, cultured and sequenced. Christa Schleper

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Moranella endobia that resides within life in 1977 and distinguished three a bacterium called Tremblaya princeps domains of life.) A third category which in turn resides within a mealy- considers misuse of terminology. bug insect cell. Unsurprisingly, he “Primitive carries too many connota- noted, the metabolic pathways in the tions,” he said. “Organisms that exist mealybug are “patchwork patterns today are not primitive, but may of genes in different places,” which contain ancestral features.” Similarly, makes it difficult to predict the sources he questioned if describing an organ- and locations of the functional genes. ism as “higher” meant it was more John McCutcheon evolved than a “lower organism.” Miscommunications about Eisen conceded that communicating A Patchwork of Pathways science accurately can be a challenge, Echoing Ettema’s talk, John Mc- Evolution but consistently making exceptions is Cutcheon of the University of Montana The Twisted Tree of Life Awards not helpful. “It’s important to be aware focused on the role of endosymbiosis in began when Jonathan Eisen of the of the risks of doing it wrong,” he said, the evolution of eukaryotes. He outlined University of California, Davis became recommending that researchers pay three important endosymbiotic events in frustrated by the inaccuracies he attention to how the science is pre- the history of life: the rise of all photo- saw in the news about evolution sented in press releases as they are synthetic eukaryotes; the evolution of and evolutionary findings. One of likely to be the foundation for media eukaryotes; and, the rise of all sap the problems, and thus an Award coverage and thus, public interest. feeding insects. (Pro tip from McCutch- category, is that people assume that eon: “You cannot feed an animal on Darwin is synonymous with evolution. plant sap alone — it’s the equivalent As in, he said, “If Darwin got some- of trying to raise a child on 7-Up.”) thing wrong in the 1850s, then all McCutcheon shared two anecdotes evolution is wrong… We should as part of his lab’s efforts to under- get back to debating the tree of life.” stand how endosymbiont genomes can The eponymous category of the be reduced from thousands of genes awards arose from frequent news down to hundreds. One of McCutch- reports that point out life is categorized eon’s examples of an endosymbiotic into five kingdoms of life. (For the system involves a bacterium called record, Carl Woese redrew the tree of Jonathan Eisen

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2019 JGI Meeting human health applications, specifi- performance computing to population- cally, to uncover the genes involved in scale genomic datasets. Genomics at the Exascale opioid addiction. The work done as a joint initiative between the Depart- Select videos from the Meeting are Dan Jacobson spoke about being ment of Energy and the US Veterans available on JGI’s YouTube channel at part of the team at Oak Ridge National Administration aims to improve http://bit.ly/JGI2019videos. Laboratory that broke the exascale healthcare outcomes for Veterans. barrier in 2018. They used the Summit The ORNL team that included supercomputer to carry out nearly Jacobson and JGI’s Chief Informatics 2 quadrillion (a billion billion) calcula- Officer Kjiersten Fagnan won a 2018 tions per second while conducting ACM Gordon Bell at the International genomic data analyses with datasets Conference for High Performance containing millions of genomes to Computing, Networking, Storage and uncover hidden networks of genes. Analysis (SC18) Conference. Address- Having a supercomputer that can ing the JGI meeting attendees, Jacob- process population-scale genomic son counted the win as the first ever datasets meant Jacobson and his for genomics and systems biology, colleagues naturally transitioned to outlining the work that applied high- Dan Jacobson and Kjiersten Fagnan

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a community effort to develop guidelines and best practices for defining virus data quality. In a Nature Biotechnology paper, JGI partnered with a number of virus experts; as well as representatives from the Genomic Standards Consor- tium (GSC), an open-membership working body that engages the research community in the standards development process; and the International Committee on Taxono- my of Viruses, the premier authority on the official taxonomy of viruses which is currently re-evaluating virus classification based on sequence- based information. (Learn more at jgi.doe.gov/defining-quality-virus- Left to Right: Rex Malmstrom, head of Micro-Scale Applications; Emiley Eloe-Fadrosh, head of the Metagenome Program; and, research scientist Simon Roux. datasets.) Perspectives of Innovation genomes directly from the environ- Unwrapping Complex In a special issue of mSystems ment and focuses on sequence reads published May 14, 2019, JGI to link mobile elements such as Mechanisms of Genome-Wide researchers were among the authors plasmids to microbial host cells. Regulation who offered perspectives on what In a separate article, research The JGI’s 1000 Fungal Genomes the next five years of innovation scientist Simon Roux, a member initiative is uncovering the true could look like. of Eloe-Fadrosh’s Environmental diversity of the fungal kingdom. In one article, Micro-Scale Genomics group, made a pitch The abundance of fungal genomes Applications head Rex Malmstrom for readers to get involved in the underscores the need for a more and Metagenome Program head developing field of virus ecogenomics. comprehensive exploration of genomic Emiley Eloe-Fadrosh outlined more While microbes regulate the planet’s DNA modifications (epigenome). The targeted approaches to reconstruct biogeochemical cycles, viruses best-known example of a modified individual microbes in an environ- infecting microbes shape global DNA base is a methylation of the mental sample beyond the tried- ecological and environmental processes, base cytosine at the 5th position and-true method of traditional especially by modifying host cell on its carbon ring, or 5mC. In many shotgun metagenomics. One approach metabolism and altering cell fitness. organisms, 5mC is an important uses fluorescence-activated cell As the vast majority of viruses remain piece of how they regulate their sorting (FACS) to sort cells into uncultivated, Roux outlined what’s genomes, but is not well understood several small pools before sequenc- been achieved thus far based on in fungi. ing to recover rare microbes. The computational predictions, and future In Nature Ecology & Evolution, technique was applied to a recent directions integrating computational a team led by Robert Schmitz at the Nature Communications paper, and experimental approaches with the University of Georgia and including uncovering giant virus sequences in aim of eventually studying virus-host JGI researchers conducted the largest soil for the first time. (Learn more dynamics in nature. analysis to date of 5mC, an impor- at jgi.doe.gov/hidden-giant-virus- A comprehensive map of viruses tant piece of the epigenome. Across forest-soils.) including host information, Roux the fungal tree of life, they tracked A second approach known as said, would be the foundation upon the evolution of 5mC pathways across DNA stable isotope probing (DNA which researchers can develop 528 species. SIP) relies on incubating DNA with high-throughput and high-resolution The researchers found that unlike isotopically-labeled compounds to studies of interactions between host most flowering plants and animals, link active microbes with specific cells and viruses in the environment. fungi lack gene body methylation. metabolic processes. A third approach Roux and Eloe-Fadrosh are also The analysis revealed that 5mC in steps away from reconstructing among the JGI researchers who led some fungal species is abundant

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for Panicum hallii towards stress Technique for Studying tolerance improvement in its more Gene Expression complex relative, the candidate bioenergy crop, switchgrass Takes Root in Plants continued from page 1 (P. virgatum). Through the Community Science Undeterred by these challenges, Program, JGI sequenced and assem- Dickel and her JGI colleagues teamed bled near-complete genomes of up with researchers from UC Davis P. hallii var. hallii (99.2% complete) who had perfected a protoplasting and P. hallii var. filipes (94.8% technique for root tissue from Arabi- complete) and resequenced a host dopsis thaliana (mouse-ear cress), of natural collections from across a species of small flowering weed that the species range. The HAL2 and serves as a plant model organism. FIL2 genomes are available on the After preparing samples of more JGI’s plant portal Phytozome. than 12,000 Arabidopsis root cells, With these high-quality reference the group was thrilled when the genomes for P. hallii, researchers can Drop-seq process went smoother identify and characterize the regulatory than expected. elements that influence adaptation “When I first spoke to Diane about and tolerance to stressors such as trying Drop-seq in plants I recognized drought. This information can be the huge potential, but I thought it applied toward improving crop yields would be difficult to separate plant in other grasses. cells rapidly enough to get useful data,” said John Vogel, JGI’s head of plant functional genomics. “I was shocked to see how well it worked Top: Spinellus fusiger. Center: Parasitella and how much they were able to parasitica. Bottom: Helicostylum cordense. learn from their initial experiment. (ZyGoLife Research Consortium on Flickr, This technique is going to be a game CC BY-SA 2.0) changer for plant biologists because it allows us to explore gene expression in repetitive DNA and transposons in without grinding up whole plant methylated cytosine clusters, rather organs, and the results aren’t mud- than in genes, which suggests that dled by signals from the few most 5mC may play a role in genome common cell types.” defense. Additionally, the team found The authors anticipate that the a correlation between genome-wide platform, and other similar RNA-seq 5mC abundance and the abundance technologies, will eventually become of specific 5mC methyltransferase routine in plant investigations. “We (MTase) variants. also showed that you can use these technologies to understand how A Model System for Perennial plants respond to different environ- mental conditions at a cellular level Grasses — something many plant biologists In Nature Communications, at Berkeley Lab are interested in a team led by Tom Juenger of the because being able to grow crops University of Texas (UT) at Austin under poor environmental conditions, and including JGI researchers such as drought, is essential for our reported the culmination of nearly continued production of food and a decade of work to develop genom- biofuel resources,” Dickel said. Panicum hallii var. filipes (left) and Panicum ic resources for drought tolerance hallii var. hallii (right) grown under controlled Full story at newscenter.lbl. in perennial grasses. The team is greenhouse conditions in Austin, Texas. gov/2019/05/16/new-technique-plant- applying the resources developed (Amalia Díaz) rna.

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Register Now! The 15th Annual DOE Joint Genome SAVE THE DATES! Find out which Institute upcoming conferences Genomics of MARCH 23 – 27, 2020 will have a JGI presence: Energy & ASM Microbe 2019 Environment June 20–24, 2019 Meeting in San Francisco, CA: Oakland Marriott City Center www.asm.org/Events/ASM-Microbe/ The Integrative Genomics Building (IGB), the new Home Watch this site! home of JGI and KBase usermeeting.jgi.doe.gov at Berkeley Lab Attend the IMG Workshop and make sure to stop by Booth 5132!

19-JG-5821 2019 Synthetic Biology: Engineer- ing, Evolution & Design (SEED) Congratulations to the JGI 2019 Annual Meeting Poster Winners! June 23–27, 2019 Recognizing scientific posters that group shot) of the University of in , NY presented particularly compelling or Texas-Austin during the JGI Genomics synbioconference.org/2019 novel research in the field of microbial of Energy & Environment Meeting. genomics, Microbial Genomics, an Both received a $200 cash price Society for Industrial Microbiol- open access and open data journal and a certificate. ogy and Biotechnology (SIMB) published by the Microbiology Society, At the JGI Genomics of Energy Annual Meeting awarded a prize at the New Lineages & Environment Meeting, the Best July 21–24, 2019 of Life (NeLLi) Symposium to Haley Student Poster Award went to Lazarus in Washington DC www.simbhq.org/annual/ Sapers of CalTech (right), seen with Takawira (right) of the University of NeLLi organizer Tanja Woyke (left). Pretoria, while the Best Overall Poster Plant Biology 2019 Another prize was awarded to Matthew Award went to Erin Nuccio of Law- August 3–7, 2019 Deaner (second from right in the rence Livermore National Laboratory. in San Jose, CA: plantbiology.aspb.org Make sure to stop by the JGI/KBase Booth 607!

Microbial Genomics & Metagenomics (MGM) Workshop November 4–8, 2019 in Berkeley, CA: Register now: mgm.jgi.doe.gov JGI Strategic Plan JGI has released its newest 5-Year Strategic Plan: Beyond Basepairs — A Vision for Integra- Contact The Primer tive and Collaborative Genome Science. New David Gilbert, Managing Editor areas of emphasis include JGI’s emerging [email protected] leadership role in a Microbiome Data Science Massie Santos Ballon, Editor effort (pages 37-39) and the launching of a Secondary Metabolites research group (pages 47-49). Download a copy at 2019_JGI-Strategic-Plan.pdf.

19-JGI-60030

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