DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    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

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

News & Publications
Home › News Releases › Unraveling the Threads: Simplest cotton genome offers clues for fiber improvements

December 19, 2012

Unraveling the Threads: Simplest cotton genome offers clues for fiber improvements

news_12_12_19-3

DOE JGI Plant Program head Jeremy Schmutz. (Holly Ralston, Director of Communications, HudsonAlpha)

From the stockings decorating mantles to the new outfits in display windows calling to shoppers, cotton is woven into the fabric of the holiday season. For bioenergy researchers, however, fiber composition matters more than color and texture as each cotton strand is composed of more than two dozen coils of cellulose, a target biomass for next-generation biofuels.

In the December 20, 2012 edition of Nature, an international consortium of researchers from 31 institutions including a team from the U.S. Department of Energy Joint Genome Institute (DOE JGI) present a high-quality draft assembly of the simplest cotton (Gossypium raimondii) genome. Additionally, the team compared the genome from this ancestral species indigenous to the Americas to several other sets of cotton data contributed by the U.S. Department of Agriculture (USDA). The results have allowed the researchers to trace the evolution of cotton over millions of years from wild varieties to the domesticated species that are now associated with textile production.

Growing, processing and manufacturing cotton is a major global industry. In the United States, more than 200,000 domestic jobs are related to cotton production and processing, with an aggregate influence of about $35 billion on the annual U.S. gross domestic product. The cotton fiber grown is valued at about $6 billion per year, with cottonseed oil and meal byproducts worth nearly another $1 billion. U.S. textile mills convert much of the cotton processed annually into apparel.

news_12_12_19-2

Cotton boll (Texas A&M AgriLife Research photo by Kathleen Phillips)

The cotton plants seen growing in typical fields in the U.S. are polyploids, hybrids of two types of cotton (cotton A and cotton D) with multiple copies of their genomes or chromosome sets. As one of the closest extant relatives of the tetraploid cotton genome (containing four sets of chromosomes), the diploid G. raimondii was selected for sequencing in part because it has a smaller genome and fewer repetitive elements than A-genome cotton and is much less complex than the polyploid cotton. D-genome cotton does not produce spinnable fibers, unlike A-genome cotton. Having data from multiple genomes for reference, such as those provided by USDA for this study, enabled the team to trace cotton’s lineage, the evolution of hybrids and the gene duplications that allowed fiber development.

“This cotton data will help accelerate the study of gene function, particularly cellulose biosynthesis, the understanding of which is fundamental to improved biofuels production,” said Jeremy Schmutz, head of the DOE JGI Plant Program and a faculty investigator at the HudsonAlpha Institute for Biotechnology, who led the effort to sequence and assemble the genome. “In addition, the unique structure of the cotton fiber makes it useful in bioremediation, and accelerated cotton crop improvement also promises to improve water efficiency and reduce pesticide use.”

news_12_12_19-1

Cotton field. (David Nance, USDA)

The DOE JGI’s contribution of sequencing and assembling the 760-million basepair genome stems from a Community Sequencing Program proposal led by University of Georgia professor Andrew Paterson. “This study represents the first time that a polyploid plant was compared to its progenitors over the entire genome,” he said. “This study reveals evolutionary processes salient to all plants and provides a strategy to better understand the genome of many other crops, such as canola, wheat, and peanut.”

Learning more about the genetic contributions of the D- and A-genomes to the common cotton species can help researchers improve fiber traits. One anecdote shared by Jay Keasling, Associate Laboratory Director for Biosciences at Lawrence Berkeley National Laboratory and CEO of the Joint BioEnergy Institute, is a reminder that the cellulose chains comprising his cotton shirt withstand repeated laundering. The story helps people understand the challenges involved in breaking down and cost-effectively converting cellulosic biomass such as plant matter into biofuels.

Don Jones, Director of Agricultural Research at Cotton Incorporated, said this G. raimondii gold standard genome will be the foundation for sequencing upland cotton, G. hirsutum, that makes up most of the worldwide field crop. Another species, G. barbadense, produces Pima cotton but accounts for less than two percent of the cotton crop. “This sequence is a cornerstone that will help advance our knowledge so we more thoroughly understand the biology that leads to enhanced yield, improved fiber quality, and better stress tolerance, all improvements that will benefit growers in the not-too-distant future.”

Schmutz said this is a good example of a project in which the DOE’s genomic contributions were matched by resources from the research community. These include genetic maps, RNA sequencing, additional genomic sequence and detailed genomic analysis, allowing a more detailed and meaningful interpretation of the results. Aside from the DOE JGI, the University of Georgia, the USDA, and Cotton Incorporated, other public and private agencies that participated in this project include the Iowa State University, Mississippi State University, the Consortium for Plant Biotechnology Research and the U.S. National Science Foundation.

Schmutz talks about the cotton genome project on YouTube at http://bit.ly/JGI-cotton-video 

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)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

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

Related Content:

JGI announces 2023 CSP Functional Genomics awardees

Digital index card with JGI logo reads: Community Science Program (FY23) Congratulations to our CSP Functional Genomics recipients! Picture from left to right: (top) Thom Booth, Gabriel Castrillo, Han Li; (bottom) Jorge A. Marchand, Emre Özdemir, Fong Tian Wong

Researching and Solving Real-World Problems with the 2023 JGI-UC Merced Interns

2023 JGI-UC Merced interns (Zhong Wang/Berkeley Lab)

RECAP: Multi-Omic Journeys with 2023 JGI Annual Meeting Keynotes

Bruce Hungate stands at a podium and gesticulates as he discusses microbes.

For the Tiniest Archaea, A Genomic Switch of Friend or Foe

A grey microscopy photo taken at micron-scale. Microbes shown are small, round and slightly spiky in shape.

Doubling Down on Known Protein Families

An illustration of a microscope emitting a beam of light that hits a small, nondescript item.

The JGI announces 2024 awardees for our Community Science Program annual call

A series of headshots: From left to right: [above] Olivia Ahern, Adriana Corales, Hugh Cross, Megan DeMarche, Joanne Emerson, Matthew Hudson, Megan Keller and Julia Kelliher; [below] Vassili Kouvelis, Seppe Kuehn, Tesfaye Mengiste, Egbert Schwartz, Hannah Schulman, Bram Stone and Jana Voriskova
  • 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