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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
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    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

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Home › Webinars › Webinar: PhycoCosm Tutorial

March 22, 2021

Webinar: PhycoCosm Tutorial

Learn more about JGI’s PhycoCosm data portal, an interactive collection of sequenced algal genomes, omics data and comparative analysis tools.

Reference: A One-Stop Shop for Analyzing Algal Genomes

Questions and Answers

1. Q(uestion): Why would your Tree ever differ from NCBI Taxonomy?
A(nswer): If you find that our trees are incorrect or need to be changed, please contact us and we’ll work work it out

2. Q(uestion): Do you publish the data sets the trees are based upon?
A: This is still work in progress as new genomes are being added. We do plan to publish the tree or their parts and data it is based on

3. Q(uestion): Can you please explain again how did you pick genomes to be on the genomes portal? For the taxa I work on, there are 7 genomes on NCBI but your portal has only 2 of them.
A: Watch the video (above) for the answer provided by Sara

4. Q(uestion): Are all CSP produced data automatically assembled and run through your annotation pipeline then added to PhycoCosm (if relevant)?
A:
For every genome that we sequence, we provide full analysis (assemble, annotate, work on initial analysis) and share data in PhycoCosm.
For genomes not sequenced by JGI, if PIs are interested are working with us please contact me at ivgrigoriev@lbl.gov

5. Q: If we have RNAseq or proteome data that is based on a model that is not based on a genome model with PhycoCosm, how do we go about getting it in your system?
A: I think the best way is to contact us for multiomics visualization as we want to support you in getting these data on our system. If it’s not based on the gene model, that should be ok generally. We can work with you to re-map the data. If your rna-seq data doesn’t necessarily agree, we also have a way to do manual annotation – not covered in these tutorials

6. Q: On the genome synteny page, would it be possible to add a feature to look for synteny of the target genome with itself, to identify regions that might be duplicated?
A: Yes, we do routinely calculate self-alignments, usually in the dropdown of available targets on the synteny page.

7. Q: What is success rate for CSP? What makes a successful CSP?
A: Reminder: two calls for proposals are open right now – large scale CSP and FICUS with March 24 and March 17 deadlines. 25-30% of proposals are selected, pretty high in comparison to other funding agencies. The JGI doesn’t fund research; we provide the resources for free.

8. Q: What makes a successful project?
A: Combination of:

  • DOE mission relevance
  • Science
  • User community – trying to produce resources for large groups of people. Talk to collaborators and colleagues

9. Q: Only algal genomes in PhycoCosm?
A: PhycoCosm is devoted to algae (photosynthetic eukaryotes not including plants), so populated by algal genomes thus defined. We also have some reference plant genomes to help with comparative studies of algae and we have various protists such as oomycetes. We think they’re valuable for comparative studies (see video for Alan’s response)

 

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