DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

    (PXFuel)
    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.

    More

    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.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

    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.

    More

    A plantation of poplar trees. (David Gilbert)
    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.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    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.

    More

    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.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    screencap from Amundson and Wilkins subsurface microbiome video
    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.

    Read more

    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.

    More

    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.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    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.

    More

    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.

    More

Our Science
Home › Science Highlights › Speciation Driven by Alleles Adapted to Local Conditions

April 3, 2017

Speciation Driven by Alleles Adapted to Local Conditions

Genome sequence analysis provides first evidence that linked, locally adapted alleles exist first, and subsequently are captured within a new, selectively-favored inversion.

The Science

A team of scientists investigated the pathway by which chromosomal inversions – in which a segment of the chromosome was removed, flipped and then re-inserted – contribute to speciation in nature.

For this study, researchers planted a test population in a mountain-top meadow near the Lost Trail Pass ski resort in the mountains of Montana. To water these transplants, they lugged nine empty garbage cans up the mountain and filled them with snow to water the plants throughout the summer. (Tom Mitchell-Olds)

For this study, researchers planted a test population in a mountain-top meadow near the Lost Trail Pass ski resort in the mountains of Montana. To water these transplants, they lugged nine empty garbage cans up the mountain and filled them with snow to water the plants throughout the summer. (Tom Mitchell-Olds)

The Impact

This study offers the first direct evidence showing that QTLs, genome regions on chromosomes to which genetic traits can be mapped, are a driving force behind speciation. While it’s known that chromosomal inversions contribute to speciation, it had not been clear whether or not this occurs due to: 1) a slow accumulation of mutations on older inversions; or, 2) young inversions that capture QTLs during the beginning stages of speciation.

Summary

On the slopes of the Northern Rocky Mountains, the flowering mustard plant Boechera stricta is undergoing a quiet transformation – that is, evolving into a fitter species better adapted to its local environment. Led by Thomas Mitchell-Olds of Duke University, a team including researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, analyzed the mechanisms by which Boechera stricta living in a hybrid zone in the Northern Rocky Mountains experienced positive directional selection.

Creek-side habitat near Lost Trail Pass ski resort in Montana. (Tom Mitchell-Olds)

Creek-side habitat near Lost Trail Pass ski resort in Montana. (Tom Mitchell-Olds)

As part of the DOE JGI’s Community Science Program and Emerging Technologies Opportunity Program, the researchers sequenced and analyzed the genome of Boechera stricta, a relative of the model plant Arabidopsis. With the genome in hand, they used techniques including gene mapping and chromosome painting methods to identify a major chromosomal inversion that controls ecologically important traits in the plant. They tested for QTLs—regions of the genome where the DNA codes for genetic traits—in Boechera stricta’s chromosomal inversion. They found several linked QTLs that changed ecologically important characteristics of the plant such as flowering time and plant size, enabling it to adapt to its local environment, which in turn increased its fitness.

“Here, in Boechera stricta we are capturing that moment of selection – the moment when the subpopulation with the inversion takes over from the pre-inversion genotype and outcompetes it,” said DOE JGI Plant Program Head Jeremy Schmutz, a co-author on the study. “The inversion fixes a set of alleles in the population. Here the set of fixed alleles improves survivability over the previous genotypes.”

The knowledge gained from this study, published in the April 3, 2017 issue of the journal Nature Ecology & Evolution, “gives evolutionary biologists experimental evidence showing how chromosomal changes contribute to adaptation and speciation. Furthermore, the genome sequence will help us understand how Boechera species are able to reproduce asexually by seeds, a process that can be used by farmers to speed up crop improvement practices,” said senior author and DOE JGI collaborator Thomas Mitchell-Olds of Duke University.

Contacts

Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov

Jeremy Schmutz
Plant Program Head
DOE Joint Genome Institute
jschmutz@hudsonalpha.com

Funding

  • DOE Office of Science
  • National Science Foundation
  • EMBO
  • Taiwan Ministry of Science and Technology
  • Swedish Research Council
  • Czech Science Foundation
  • National Institutes of Health
  • AXA Research Fund
  • Arizona Genomics Institute, University of Arizona

Publications

  • Lee CR et al. “Young inversion with multiple linked QTLs under selection in a hybrid zone.” Nat. Ecol. Evol. (2017) doi: 10.1038/s41559-017-0119

Related Links

  • Boechera stricta study on plant flowering time: http://jgi.doe.gov/soil-microbiomes-can-set-plant-flowering-time/
  • Boechera stricta genome on Phytozome: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Bstricta
  • Community Science Program: http://jgi.doe.gov/user-program-info/community-science-program/
  • Emerging Technologies Opportunities Program: http://jgi.doe.gov/doe-joint-genome-institute-expands-capabilities-via-new-partnerships/

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

Filed Under: Science Highlights

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

Soil virus offers insight into maintaining microorganisms

Silver age of GOLD introduces new features

Abstract image of gold lights and squares against a black backdrop

Virus Discoveries that Keep Getting Bigger

And illustration of a giant virus in purple and blue tones.

Model fern reveals insight into DNA thievery in ferns

A green fern against a black backdrop

Understanding Wildfire Recovery, Starting in Soil

A photograph of the forest floor, covered in pine needles, with burned trees in the background.

Extracting the Secrets of Secondary Metabolites

A graphic flowchart showing how CRAGE and CRISPR work together
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California