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 › Beyond Genomics—DOE JGI leads method validation effort in Metatranscriptomics

September 20, 2010

Beyond Genomics—DOE JGI leads method validation effort in Metatranscriptomics

Ultra-high throughput DNA sequencing platforms that allow researchers to sequence the genetic code of organisms at lightning speed for just pennies are enabling more focused genomic studies on a massive scale. One example involves the transcriptome, a tiny but complex fraction of the complete genetic sequence that is transcribed into different types of RNA molecules. These molecules provide researchers with information about what genes are turned on and off under various conditions, and what the functions of these genes are.

Researchers focus on the messenger RNA (mRNA), which transfer the genetic information from the DNA to functional proteins. The bulk of cellular RNA is composed of ribosomal RNA (rRNA), however, which researchers prefer to remove before sequencing to increase mRNA detection. There are several techniques to do this but, noted Phil Hugenholtz, formerly of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and now director of the Australian Center for Ecogenomics at the University of Queensland, Australia, determining which method to use can be tricky.

shaomei

Shaomei He, first author of the study

“As a user facility, the DOE JGI is getting an increasing number of requests for metatranscriptomic analyses. Almost always associated with these requests are questions about what rRNA depletion methods should be used to enrich for mRNAs,” he said, adding that, “there is very little hard data on which method to use and most researchers base their decision on largely incomparable anecdotal evidence.”

To help researchers interested in submitting metatranscriptomic projects to the DOE JGI, Hugenholtz and his DOE JGI colleagues validated two popular rRNA removal methods used by researchers. The methods were tested using commercially available kits: Ambion’s MICROBExpress™ Bacterial mRNA Enrichment Kit and Epicentre’s mRNA-ONLY™ Prokaryotic mRNA Isolation Kit. The Ambion kit uses a technique called subtractive hybridization, which involves oligonucleotide probes that target rRNA sequences, while the Epicentre kit preferentially degrades processed rRNAs using enzymes called exonucleases.

Shaomei He, an Energy Biosciences Institute-funded postdoctoral researcher working at the DOE JGI and first author of the study published online September 19 in Nature Methods,said the validation study was prompted in part by researchers interested in having the DOE JGI conduct metatranscriptomic analyses and asking for recommendations on how to enrich the mRNA molecules. “When people use these methods there’s no systemic analysis to show if there’s an associated bias,” she said. “The two questions we wanted to answer in this project were: 1) how efficient are these methods at rRNA removal? and; 2) do they introduce any biases in mRNA?”

The team noted that both rRNA removal techniques have limitations. For example, said He, the hybridization kit uses generic probes that miss some bacteria and all archaea while the exonuclease kit also removes partially degraded mRNA. “Ultimately what you use depends on samples of interest and the biological question being asked,” she said.

He and her colleagues tested both rRNA removal methods using two artificial communities made by mixing RNA from multiple microbial species whose genomes had been sequenced, some of them at the DOE JGI. The first community was composed of five bacteria while the second community also included an archaeal species. They ran several trials using each method singly and in combinations.

Mburtonii_cells

Halorhabdus utahensis AX-2T (Scanning electron micrograph
provided by Manfred Rohde, Helmholtz Centre for Infection Research, Braunschweig)

One of the team’s findings was that rRNA removal efficiency depends on a combination of microbial community composition and RNA integrity. Another was that though some researchers favor combining both techniques, a process that can produce higher levels of rRNA removal, it also introduces a large skew in mRNA relative abundance.

The final outcome favors the use of the subtractive hybridization method by itself, which adequately preserved mRNA relative abundance for quantitative analyses, and He noted that researchers are already working on ways to improve the subtractive hybridization method. “The limitations of the commercial kit associated with its generic probes are likely to be overcome by a sample-specific hybridization approach recently developed by Ed DeLong’s lab at MIT, especially if the community is dominated by archaea,” she said.

Other authors on the paper include DOE JGI’s Kanwar Singh, Jeff Froula, Suzan Yilmaz, Susannah Tringe, Zhong Wang, Feng Chen and Erika Lindquist.  Omri Wurtzel and Rotem Sorek from the Weizmann Institute of Science (Israel) also collaborated on the paper. [Download the Nature Methods paper.]

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:

You can move, but you can’t hide

Illustration of a magnifying glass identifying viruses and plasmids.

JGI announces second round of 2023 New Investigator awardees

From left to right: [above] Emma Bell, Mallory Choudoir, Sneha Couvillion, Tobin Hammer, Christina Hazard, Rachel Mackelprang, Brook Moyers, Mei, Ran,; [below] Benjamin Peterson, Dacheng Ren, Allison Rober, Neal Scott, Chikae Tatsumi, Vojtech Tlaskal, Fernando Torralbo, Luis Felipe Valdez-Nuñez

A Collaboration to Improve Plant Genome Annotations Across Species

A tiled collage of square photos of different plants - soybeans, and sorghum, for example.

From Berkeley to Binghamton: Tracking Strawberry Evolution

iPHoP: A Matchmaker for Phages and their Hosts

iPHoP image (Simon Roux)

Supercharging SIP in the Fungal Hyphosphere

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.
  • 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