Igor Grigoriev
Adjunct Professor / Senior Scientist / Program Head
Igor Grigoriev joined the PMB faculty as an adjunct professor in 2013. He worked at the Department of Energy's Joint Genome Institute (JGI) since 2003 participating in the Human Genome Project and leading annotation of diverse eukaryotic genomes, from protists to plants (genome.jgi.doe.gov). In 2009, he started the JGI Fungal Genomics program, which led to the large-scale projects like "1000 Fungal Genomes" or "Fungal mini-ENCODE", and delivered 1500+ annotated fungal genomes and multi-omics datasets integrated in MycoCosm portal with interacting comparative genomics tools. He also leads annotation of a large collection of algal genomes assembled in PhycoCosm portal. Prof. Grigoriev organized more than 50 genomics workshops, engaged several thousand researchers around the world in genome projects, published 250+ papers (46K+ citations, H-index=86), and was recognized by Thomson Reuters and Web of Science as Highly Cited Research (top 1%) in 2014-2019.
Computational genomics: Grigoriev's lab develops computational methods and tools for gene prediction, genome annotation, comparative genomics, and functional multi-omics analyses. These methods were applied to annotation and analysis of a large number of diverse genomes sequenced by JGI and elsewhere. The most recent developments include genome-based prediction of fungal lifestyle using machine learning approaches.
Fungal genomics: There are more than 1.5 million fungal species and they play a critical role in shaping the Earth's ecosystems. A better understanding of pathogens and symbionts is critical for the sustainable growth of plants. Fungi are the most efficient degraders of plant biomass to enable conversion into bioenergy and bioproducts. Many new metabolic processes and enzymes are encoded in fungal genomes. Fungal genomics may offer answers to critical areas of research, including food, medicine, energy, and the environment. (see examples here)
Algal genomics: Algae are a phylogenetically diverse group of eukaryotes that are collectively responsible for 50% of photosynthesis on Earth. The enormous phylogenetic and functional diversity of algae require a systematic genomics exploration to better understand their complex evolution, mechanisms of photosynthesis, and potential for bioenergy, bioproducts, and biomanufacturing. (see examples here)
EDUCATION
- Postdoctoral Training in Computational Structural Genomics, UC Berkeley
- Ph.D. in Molecular Biology, Research Institute for Genetics and Selection of Industrial Organisms, Moscow, Russia
- B.S. / M.S. in Biophysics, Moscow Engineering Physics Institute, Moscow, Russia
SELECTED PUBLICATIONS
Click here for a complete list of publications
- Haridas et al (2020) 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens. Stud Mycol. 96:141-153.
- Wu et al (2020) The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus. Proc Natl Acad Sci U S A. 117(11):6003-6013.
- Kjærbølling et al (2020) A comparative genomics study of 23 Aspergillus species from section Flavi. Nature Commun. 11(1):1106.
- Nibert et al (2019) Mitovirus and mitochondrial coding sequences from basal fungus Enthomophthora muscae. Viruses. 11(4):351
- Calhoun et al (2019) Yeasts and how they came to be. Nature Rev Microbiol. 17(11):649.
- Krizsán et al (2019) Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi. Proc Natl Acad Sci U S A. 116(15):7409-7418.
- Varga et al (2019) Megaphylogeny resolves global patterns of mushroom evolution. Nature Ecol Evol. 3(4):668-678.
- Bewick et al (2019) Diversity of cytosine methylation across the fungal tree of life. Nature Ecol Evol. 3(3):479-490.
- Murat et al (2018) Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle. Nature Ecol Evol. 2(12):1956-1965.
- Vesth et al (2018) Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nature Genet. 50(12):1688-1695.
- Weiss et al (2018) Genetic dissection of interspecific differences in yeast thermotolerance. Nature Genet. 50(11):1501-1504.
- Ahrendt et al (2018) Leveraging single-cell genomics to expand the fungal tree of life. Nature Microbiol. 3(12):1417-1428.
- Krassowski et al (2018) Leveraging single-cell genomics to expand the fungal tree of life. Nature Microbiol. 3(12):1417-1428.
- Lewin et al (2018) Earth BioGenome Project: Sequencing life for the future of life. Proc Natl Acad Sci U S A. 115(17):4325-4333.
- Kjærbølling et al (2018) Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proc Natl Acad Sci U S A. 115(4):E753-E761.
- Mondo et al (2017) Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. Nature Commun. 8(1):1843.
- Sipos et al (2017) Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nature Ecol Evol. 1(12):1931-1941
- Haitjema et al (2017) A parts list for fungal cellulosomes revealed by comparative genomics. Nature Microbio 2:17087.
- Mondo et al (2017) Widespread adenine N6-methylation of active genes in fungi. Nature Genet. 49(6):964-968.
- Mock et al (2017) Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature. 541(7638):536-540.
- Lastovetsky et al (2016) Lipid metabolic changes in an early divergent fungus govern the establishment of a mutualistic symbiosis with endobacteria. Proc Natl Acad Sci U S A. 113(52):15102-15107.
- Peter et al (2016) Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nature Commun. 7:12662
- Riley et al (2016) Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A. 113(35):9882-9887.
- Corrochano et al (2016) Expansion of signal transduction pathways in fungi by extensive genome duplication. Curr Biol. 26(12):1577-1584.
- 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.
- Kohler et al (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nature Genet. 47(4):410-415.
- Hurley et al (2014) Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proc Natl Acad Sci U S A. 111(48):16995-7002.
- Nagy et al (2014) Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nature Commun. 5:4471.
- Riley et al (2014) 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. 111(27):9923-9928.
- Grigoriev et al (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 42(1):D699-704.
- Tisserant et al (2013) Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A. 110(50):20117-20122.
- Read et al (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499(7457):209-213.
- Simakov et al (2012) Insights into bilaterian evolution from three spiralian genomes. Nature. 493(7433):526-531.
- Curtis et al (2012) Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature. 492(7427):59-65.
- Ohm et al (2012) Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen dothideomycetes fungi. PLoS Pathog. 8(12):e1003037
- Morin et al (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci U S A. 109(43):17501-6.
- Floudas et al (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science. 336(6089):1715-1719.
- Berka et al (2011) Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nature Biotechnol. 29(10):922-927.
- Druzhinina et al (2011) Trichoderma: the genomics of opportunistic success. Nature Reviews Microbiol. 9(10):749-759.
- Wohlbach et al (2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc Natl Acad Sci U S A. 108(32):13212-13217.
- Eastwood et al (2011) The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science. 333(6043):762-765.
- Banks et al (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 332(6032):960-963.
- Hu et al (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genet. 43(5):476-481.
- Gobler et al (2011) Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc Natl Acad Sci U S A. 108(11):4352-4357.
- Colbourne et al (2011) The ecoresponsive genome of Daphnia pulex. Science. 331(6017):555-561.
- Ohm et al (2010) Formation of mushrooms and lignocellulose degradation encoded in the genome sequence of Schizophyllum commune Nature Biotech. 28(9):957-963
- Prochnik et al (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science. 329(5988):223-226.
- Hellsten et al (2010) The genome of the Western clawed frog Xenopus tropicalis. Science. 328(5978):633-636.
- Fritz-Laylin et al (2010) The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell. 140(5):631-642
- Worden et al (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science. 324, 268-272.
- Paterson et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature. 457, 551-556.
- Bowler et al (2008) The Phaeodactylum genome reveals the dynamic Nature and multi-lineage evolutionary history of diatom genomes. Nature. 456, 239-244.
- Srivastava et al (2008) The Trichoplax Genome and the Nature of Placozoans. Nature. 454, 955-960.
- Kalyuzhnaya et al (2008) High-resolution metagenomics targets specific functional types in complex microbial communities. Nature Biotechnology. 26, 1029-1034.
- Putnam et al (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature. 19, 1064-1071
- Martinez et al (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).Nature Biotechnology. 26, 553-560.
- Martin et al (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 452, 88-92.
- King et al (2008) The genome of the choanoflagellate. Nature. 451, 783-788.
- Rensing et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 319, 64-69.
- Merchant et al (2007) The Chlamydomonas genome reveals evolutionary insights into key animal and plant functions. Science, 318, 245-250.
- Putnam et al (2007) Sea anemone genome reveals ancestral eumetazoan gener epertoire and genomic organization. Science. 317, 86-94.
- Palenik et al (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A. 104, 7705-7710.
- Jeffries et al (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nature Biotechnology. 25, 319 – 326.
- Makarova et al (2006) Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. U S A, 103, 15611-15616.
- Tuskan et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) Science. 313, 1596-1604.
- Tyler et al (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science. 313, 1261-1266.
- Martin et al (2004) The sequence and analysis of duplication-rich human chromosome 16. Nature. 432, 988-994.
- Schmutz et al (2004) The DNA sequence and comparative analysis of human chromosome 5. Nature 431, 268-274.
GENOME PROJECTS
- 1000 Fungal Genomes Project: nominate new species for sequencing
- MycoCosm, a fungal genomics resource: mycocosm.jgi.doe.gov
- PhycoCosm, an algal genomics resource: phycocosm.jgi.doe.gov
- JGI genome projects: genome.jgi.doe.gov
- JGI Community Science Program: calls for proposals
Igor Grigoriev
Research Focus:
Fungal and Algal Genomics, Computational Biology
E-mail
Location
Joint Genome Institute / Lawrence Berkeley National Laboratory / UC Berkeley
1 Cyclotron Road, Berkeley, California 94720
1 Cyclotron Road, Berkeley, California 94720
Phone Number
(510) 495-8336