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    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.

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

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    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.

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    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.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    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.

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    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.

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    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.

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    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.”

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    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.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    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.

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    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.

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    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.

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    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.

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Home › Our Science › Science Programs & Platforms Leads › Igor Grigoriev

Igor Grigoriev

grigoriev

Igor Grigoriev, Ph.D
Fungal Genomics Program Lead, DOE Joint Genome Institute

Following postdoctoral training and several years of work in the pharmaceutical industry, Dr. Grigoriev joined the DOE Joint Genome Institute in 2003 to participate in human genome annotation and lead annotation of over 100 diverse eukaryotic genomes from protists to plants. In 2009, he started the Fungal Genomics program to scale up sequencing and analysis of diverse fungi for related to DOE science and applications. Dr. Grigoriev organized over 30 genomics workshops and engaged over 2000 researchers around the world in genome projects, which resulted in over 50 high-profile publications. In the same vein, he and his team are working to organize research labs around large-scale, most-needed genomics projects to develop genetic blueprints for diverse algae to enable comparative and functional algal genomics.

Education

  • BA/MS in Biophysics, Moscow Engineering Physics Institute, Moscow, Russia
  • PhD in Molecular Biology, Research Institute for Genetics and Selection of Industrial Organisms, Moscow, Russia
  • Postdoctoral training in computational structural genomics, University of California, Berkeley, CA

Selected Publications

  1. Riley et al (2016) Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A. 113(35):9882-7.
  2. Corrochano et al  (2016) Expansion of signal transduction pathways in fungi by extensive genome duplication. Curr Biol. 26(12):1577-1584.
  3. Dhillon et al (2015) Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen. Proc Natl Acad Sci U S A. 112(11):3451-3456.
  4. Kohler et al  (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nature Genet. 47(4):410-415.
  5. Grigoriev et al (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res.42(1):D699-704.
  6. Riley R et al. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A. 2014; 111: 9923-9928.
  7. Tisserant E et al.  Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A. 2013; 110: 20117-20122.
  8. Read B et al. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature. 2013; 499: 209-213.
  9. Curtis BA Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature. 2012; 492: 59-65.
  10. Ohm RA et al. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen dothideomycetes fungi. PLoS Pathog. 2012; 8(12):e1003037.
  11. Floudas D et al. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science. 2012;336: 1715-1719.
  12. Berka RM et al. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnol. 2011; 29: 922-927.
  13. Eastwood DC et al. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science. 2011; 333: 762-765.
  14. Gobler CJ et al. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc Natl Acad Sci U S A. 2011; 108: 4352-4357.
  15. Banks JA et al. The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science, 2011; 332: 960-963.
  16. Colbourne JK et al. The ecoresponsive genome of Daphnia pulex. Science. 2011; 331: 555-561.
  17. Ohm RA et al. Formation of mushrooms and lignocellulose degradation encoded in the genome sequence of Schizophyllum commune. Nat Biotech. 2010; 28: 957-963.
  18. Worden AZ et al. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science. 2009; 324: 268-272.
  19. Bowler C et al. The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes. Nature. 2008; 456: 239-244.
  20. Martin F et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 2008; 452: 88-92.
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