• Publications

  • (Clicking on the reprint icon will take you to the publication reprint.)
  • Assembly and analysis of the genome of Notholithocarpus densiflorus -(Peer Reviewed Journal)
    Cai, Y., Anderson, E., Xue, W., Wong, S., Cui, L., Cheng, X., Wang, O., Mao, Q., Liu, S.J., Davis, J.T., Magalang, P.R., Schmidt, D., Kasuga, T., Garbelotto, M., Drmanac, R., Kua, C., Cannon, C., Maloof, J.N., Peters, B.A. 2024. Assembly and analysis of the genome of Notholithocarpus densiflorus. G3, Genes/Genomes/Genetics. 14(5). Article jkae043. https://doi.org/10.1093/g3journal/jkae043.
    
  • A super-pangenome of the North American wild grape species -(Peer Reviewed Journal)
    Cochetel, N., Minio, A., Guaraccino, A., Garcia, J., Figueroa-Balderas, R., Massonnet, M., Kasuga, T., Londo, J., Garrison, E., Gaut, B., Cantu, D. 2023. A super-pangenome of the North American wild grape species. Genome Biology. 24. Article 290. https://doi.org/10.1186/s13059-023-03133-2.
    
  • Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora -(Peer Reviewed Journal)
    Wang, Z., Wang, Y., Kasuga, T., Lopez-Giraldez, F., Zhang, Y., Zhang, Z., Wang, Y., Dong, C., Sil, A., Trail, F., Yarden, O., Townsend, J. 2023. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. PLoS Genetics. 19(11). Article e1011019. https://doi.org/10.1371/journal.pgen.1011019.
    
  • Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa -(Peer Reviewed Journal)
    Wang, Z., Wang, Y., Kasuga, T., Hassler, H., Lopez-Giraldez, F., Dong, C., Yarden, O., Townsend, J. 2023. Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa. Molecular Ecology. https://doi.org/10.1111/mec.17168.
    
  • Conversion of deproteinized cheese whey to lactobionate by an engineered Neurospora crassa strain F5 -(Peer Reviewed Journal)
    Poltorak, A., Zhou, X., Kasuga, T., Xu, Y., Zhiliang, F. 2023. Conversion of deproteinized cheese whey to lactobionate by an engineered Neurospora crassa strain F5. Applied Biochemistry and Biotechnology. https://doi.org/10.1007/s12010-023-04583-x.
    
  • Comparative genomic analysis of 31 Phytophthora genomes reveals genome plasticity and horizontal gene transfer -(Peer Reviewed Journal)
    Kronmiller, B.A., Feau, N., Shen, D., Tabima, J.F., Ali, S.S., Armitage, A.D., Arredondo, F., Bailey, B.A., Bollmann, S.R., Dale, A., Harrison, R., Hrywkiw, K., Kasuga, T., Mcdougal, R., Nellist, C.F., Panda, P., Tripathy, S., Williams, N.M., Ye, W., Wang, Y., Hamelin, R.C., Grunwald, N.J. 2023. Comparative genomic analysis of 31 Phytophthora genomes reveals genome plasticity and horizontal gene transfer. Molecular Plant-Microbe Interactions. 36:26-46. https://doi.org/10.1094/MPMI-06-22-0133-R.
    
  • Conversion of deproteinized cheese whey to lactobionic acid by an engineered Neurospora crassa-(Peer Reviewed Journal)
    
    
  • A rapid in vitro phenotypic assay of walnut shoots for prescreening resistance of Phytophthora pini -(Peer Reviewed Journal)
    Zaini, P.A., Lee, S.H., Leslie, C.A., Walawage, S.L., Jiang, C., Browne, G.T., Dandekar, A.M., Kasuga, T. 2021. A rapid in vitro phenotypic assay of walnut shoots for prescreening resistance of Phytophthora pini. Plant Health Progress. 22(3):235-239. https://doi.org/10.1094/PHP-05-21-0078-FI.
    
  • Innate resistance and phosphite treatment affect both the pathogen’s and host’s transcriptomes in the Tanoak-Phytophthora ramorum pathosystem -(Peer Reviewed Journal)
    Kasuga, T., Hayden, K., Eyre, C., Croucher, P., Schechter, S., Wright, J., Garbelotto, M. 2021. Innate resistance and phosphite treatment affect both the pathogen’s and host’s transcriptomes in the Tanoak-Phytophthora ramorum pathosystem. The Journal of Fungi. 7(3). Article 198. https://doi.org/10.3390/jof7030198.
    
  • Analysis of volatile profiles for tracking asymptomatic infections of Phytophthora ramorum and other pathogens in rhododendron -(Peer Reviewed Journal)
    Thompson, C., McCartney, M., Roubtsova, T., Kasuga, T., Ebeler, S., Davis, C., Bostock, R. 2021. Analysis of volatile profiles for tracking asymptomatic infections of Phytophthora ramorum and other pathogens in rhododendron. Phytopathology. https://doi.org/10.1094/PHYTO-10-20-0472-R.
    
  • Asexual evolution and forest conditions drive genetic parallelism in Phytophthora ramorum -(Peer Reviewed Journal)
    Yuzon, J., Travadon, R., Malar C, M., Tripathy, S., Rank, N., Mehl, H., Rizzo, D., Cobb, R., Small, C., Tang, T., McCown, H., Garbelotto, M., Kasuga, T. 2020. Asexual evolution and forest conditions drive genetic parallelism in Phytophthora ramorum. Microorganisms. 8(6). https://doi.org/10.3390/microorganisms8060940.
    
  • Independent whole-genome duplications define the architecture of the genomes of the devastating West African cacao black pod pathogen Phytophthora megakarya and its close relative Phytophthora palmivora -(Peer Reviewed Journal)
    Morales-Cruz, A., Ali, S.S., Minio, A., Figueroa-Balderas, R., Garcia, J.F., Kasuga, T., Puig, A.S., Marelli, J., Bailey, B.A., Cantu, D. 2020. Independent whole-genome duplications define the architecture of the genomes of the devastating West African cacao black pod pathogen Phytophthora megakarya and its close relative Phytophthora palmivora. G3, Genes/Genomes/Genetics. 10(6). https://doi.org/10.1534/g3.120.401014.
    
  • Homoethanol production from cellobionate and glycerol using recombinant Klebsiella oxytoca strains-(Peer Reviewed Journal)
    
    
  • Updated assembly of Phytophthora ramorum pr102 isolate incorporating long reads from PacBio sequencing -(Peer Reviewed Journal)
    Malar C, M., Yuzon, J.D., Panda, A., Kasuga, T., Tripathy, S. 2019. Updated assembly of Phytophthora ramorum pr102 isolate incorporating long reads from PacBio sequencing. Molecular Plant-Microbe Interactions. 32(11):1472-1474. https://doi.org/10.1094/MPMI-05-19-0147-A.
    
  • Haplotype-phased genome assembly of virulent Phytophthora ramorum isolate ND886 facilitated by long-read sequencing reveals effector polymorphisms and copy number variation -(Peer Reviewed Journal)
    Malar, M.C., Yuzon, J.D., Das, S., Das, A., Panda, A., Ghosh, S., Tyler, B.M., Kasuga, T., Tripathy, S. 2019. Haplotype-phased genome assembly of virulent Phytophthora ramorum isolate ND886 facilitated by long-read sequencing reveals effector polymorphisms and copy number variation. Molecular Plant-Microbe Interactions. 32(8):1047-1060. https://doi.org/10.1094/MPMI-08-18-0222-R.
    
  • Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids -(Peer Reviewed Journal)
    Sillo, F., Gonthier, P., Lockman, B., Kasuga, T., Garbelotto, M. 2019. Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids. Ecology and Evolution. 00:1–18. https://doi.org/10.1002/ece3.5238.
    
  • Homoethanol production from Glycerol and Gluconate using recombinant Klebsiella Oxytoca strains -(Peer Reviewed Journal)
    Tao, W., Wang, Y., Walters, E., Lin, H., Li, S., He, H., Kasuga, T., Zhiliang, F. 2019. Homoethanol production from glycerol and gluconate using recombinant Klebsiella oxytoca strains. Applied and Environmental Microbiology. 85:e02122-18. https://doi.org/10.1128/AEM.02122-18.
    
  • Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts -(Peer Reviewed Journal)
    Elliot, M., Yuzon, J., Malar, M.C., Tripathy, S., Bui, M., Chastagner, G.A., Coats, K., Rizzo, D.M., Garbelotto, M., Kasuga, T. 2018. Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts. BMC Genomics. 19:320. https://doi.org/10.1186/s12864-018-4709-7.
    
  • Effects of Phytophthora ramorum on volatile organic compound emissions of Rhododendron using gas chromatography-mass spectrometry -(Peer Reviewed Journal)
    McCartney, M., Roubtsova, T., Yamaguchi, M., Kasuga, T., Ebeler, S., Davis, C., Bostock, R. 2017. Effects of Phytophthora ramorum on volatile organic compound emissions of Rhododendron using gas chromatography-mass spectrometry. Analytical and Bioanalytical Chemistry. 410(5):1475-1487. https://doi.org/10.1007/s00216-017-0789-5.
    
  • Engineering Neurospora crassa for cellobionate production directly from cellulose without any enzyme addition-(Peer Reviewed Journal)
    Lin, H., Hildebrand, A., Kasuga, T., Zhiliang, F. 2017. Engineering Neurospora crassa for cellobionate production directly from cellulose without any enzyme addition. Enzyme and Microbial Technology. 99:25-31. doi: 10.1016/j.enzmictec.2016.12.009.
    
  • Alcohol consumption and tolerance of Neurospora crassa-(Peer Reviewed Journal)
    Lin, H., Warmack, R., Han, S., Kasuga, T., Fan, Z. 2016. Alcohol consumption and tolerance of Neurospora crassa as a potential consolidated bioprocessing microorganism. Fementation Technology. 5:136. doi: 10.4172/2167-7972.1000136.
    
  • Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum-(Peer Reviewed Journal)
    Kasuga, T., Bui, M.Q., Berhardt, E., Swiecki, T., Aram, K., Cano, L.M., Webber, J., Brasier, C., Press, C.M., Grunwald, N.J., Rizzo, D.M., Garbelotto, M. 2016. Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum. BMC Genomics. 17:385. doi: 10.1186/s12864-016-2717-z.
    
  • Cellobionic acid inhibition of cellobiohydrolase I and cellobiose dehydrogenase-(Peer Reviewed Journal)
    Hildebrand, A., Addison, J.B., Kasuga, T., Fan, Z. 2016. Cellobionic acid inhibition of cellobiohydrolase I and cellobiose dehydrogenase. Biochemical Engineering Journal. 109: 236-242. DOI: 10.1016/j.bej.2016.01.024.
    
  • Phytophthora ramorum causes cryptic bole cankers in Canyon line Oak-(Peer Reviewed Journal)
    Swiecki, T., Aram, K., Kasuga, T., Bui, M.Q., Rizzo, D., Bernhardt, E. 2016. Phytophthora ramorum causes cryptic bole cankers in Canyon line Oak. Plant Health Progress. 17:20-26.
    
  • A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia -(Peer Reviewed Journal)
    Yin, J., Chang, X., Kasuga, T., Bui, M.Q., Reid, M.S., Jiang, C. 2015. A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia. Horticulture Research. doi: 10.1038/hortres.2015.59.
    
  • Production of cellobionate from cellulose using an engineered Neurospora crassa strain with laccase and redox mediator addition -(Peer Reviewed Journal)
    Hildebrand, A., Kasuga, T., Fan, Z. 2015. Production of cellobionate from cellulose using an engineered Neurospora crassa strain with laccase and redox mediator addition. PLoS One. DOI: 10.1371/journal.pone.0123006.
    
  • Engineering Neurospora crassa for improved cellobiose and cellobionate production -(Peer Reviewed Journal)
    Hildebrand, A., Szewczyk, E., Lin, H., Kasuga, T., Fan, Z. 2015. Engineering Neurospora crassa for improved cellobiose and cellobionate production. Applied and Environmental Microbiology. 81:597-603.
    
  • A self-excising beta-recombinase/six cassette for repetitive gene deletion and homokaryon purification in Neurospora crassa -(Peer Reviewed Journal)
    Szewczyk, E., Kasuga, T., Fan, Z. 2014. A self-excising beta-recombinase/six cassette for repetitive gene deletion and homokaryon purification in Neurospora crassa. Journal of Microbiological Methods. 91(100):17-23.
    
  • Epigenetic mechanisms and the evolution of virulence -(Review Article)
    Kasuga, T., Gijzen, M. 2013. Epigenetic mechanisms and the evolution of virulence. Trends in Microbiology. 21:575-582.
    
  • Sex-linked phenotypic divergence in the hermaphrodite fungus Neurospora tetrasperma-(Peer Reviewed Journal)
    Samils, N., Gioti, A., Karlsson, M., Yu, S., Kasuga, T., Bastiaans, E., Wang, Z., Li, N., Townsend, J., Johannesson, H. 2013. Sex-linked phenotypic divergence in the hermaphrodite fungus Neurospora tetrasperma. Proceedings of the Royal Society of London: Biological Sciences. doi:10.1098/rspb.2013.0862.
    
  • PRP8 intein in cryptic species of Histoplasma capsulatum: evolution and phylogeny -(Peer Reviewed Journal)
    Theodoro, R.C., Scheel, C.M., Brandt, M.E., Kasuga, T., Bagagli, E. 2013. PRP8 intein in cryptic species of Histoplasma capsulatum: evolution and phylogeny. Infection, Genetics and Evolution. 18:174-182.
    
  • Direct cellobiose production from cellulose using sextuple beta-glucosidase gene deletion Neurospora crassa mutants -(Peer Reviewed Journal)
    Wu, W., Hildebrand, A., Kasuga, T., Xiong, X., Fan, Z. 2013. Direct cellobiose production from cellulose using sextuple beta-glucosidase gene deletion Neurospora crassa mutants. Enzyme and Microbial Technology. 18:184-189.
    
  • Efficient sequential repetitive gene deletions in Neurospora crassa -(Peer Reviewed Journal)
    Szewczyk, E., Kasuga, T., Fan, Z. 2013. Efficient sequential repetitive gene deletions in Neurospora crassa. Journal of Microbiological Methods. 92:236-243.
    
  • Detection and characterization of Histoplasma capsulatum in a German badger (Meles meles) by ITS sequencing and multilocus sequencing analysis -(Peer Reviewed Journal)
    Eisenberg, T., Seeger, H., Kasuga, T., Eskens, U., Sauerwald, C., Kaim, U. 2013. Detection and characterization of Histoplasma capsulatum in a German badger (Meles meles) by ITS sequencing and multilocus sequencing analysis. Medical Mycology. 51:337-344.
    
  • Phenotypic diversification is associated with host-induced transposon derepression in the Sudden Oak Death pathogen Phytophthora ramorum-(Peer Reviewed Journal)
    Kasuga, T., Kozanitas, M., Bui, M.Q., Huberli, D., Rizzo, D., Garbelotto, M. 2012. Phenotypic diversification is associated with host-induced transposon derepression in the Sudden Oak Death pathogen Phytophthora ramorum. PLoS One. 7:e34728.
    
  • A novel biochemical platform for fuels and chemicals production from cellulosic biomass-(Peer Reviewed Journal)
    Ziliang, F., Weihua, W., Hildebrand, A., Kasuga, T., Zhang, R., Xiaochao, X. 2012. A novel biochemical platform for fuels and chemicals production from cellulosic biomass. PLoS One. 7(2).
    
  • Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees?-(Peer Reviewed Journal)
    Luz, G., Kasuga, T., Glass, N., Taylor, J. 2011. Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees?. Biomed Central (BMC) Genomics. 12:487.
    
  • Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach-(Peer Reviewed Journal)
    Luz, G., Lee, C., Kasuga, T., Taylor, J. 2011. Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach. Biomed Central (BMC) Genomics. 12:456.
    
  • Evaluation of automated cell disruptor methods for oomycetous and ascomycetous model organisms-(Peer Reviewed Journal)
    Kasuga, T., Bui, M.Q. 2011. Evaluation of automated cell disruptor methods for oomycetous and ascomycetous model organisms. Fungal Genetics Reports. 58:4-13.
    
  • Temporal and Spatial Regulation of Gene Expression during Asexual Development of Neurospora crassa-(Peer Reviewed Journal)
    Greenwald, C.J., Kasuga, T., Glass, N., Shaw, B.D., Ebbole, D.J., Wilkinson, H.H. 2010. Temporal and Spatial Regulation of Gene Expression during Asexual Development of Neurospora crassa. Genetics. 186: 1217-1230.
    
  • Expression of Cellobiose Dehydrogenase from Neurospora crassa in Pichia pastoris and its purification and characterization -(Peer Reviewed Journal)
    
    
  • CHRONIC DISSEMINATED HISTOPLASMOSIS WITH PROLONGED LATENCY-(Peer Reviewed Journal)
    Addidle, M., Pynn, J., Skellern, P., Kasuga, T., Grimwade, K. 2010. CHRONIC DISSEMINATED HISTOPLASMOSIS WITH PROLONGED LATENCY. Journal of Internal Medicine. 61:272-274.
    
  • RELATIONSHIP BETWEEN PHYLOGENETIC DISTRIBUTION AND GENOMIC FEATURES IN NEUROSPORA CRASSA-(Peer Reviewed Journal)
    Kasuga, T., Mannhaupt, G., Glass, N.L. 2009. RELATIONSHIP BETWEEN PHYLOGENETIC DISTRIBUTION AND GENOMIC FEATURES IN NEUROSPORA CRASSA. PLoS One. 10.1371/journal.pone.0005286
    
  • TRANSCRIPTIONAL ANALYSIS OF THE REPONSE OF NEUROSPORA CRASSA TO PHYTOSHINGOSINE REVEALS LINKS TO MITOCHRONDRIAL FUNCTION-(Peer Reviewed Journal)
    Videira, A., Kasuga, T., Tian, C., Lemos, C., Castro, A., Glass, N. 2009. TRANSCRIPTIONAL ANALYSIS OF THE REPONSE OF NEUROSPORA CRASSA TO PHYTOSHINGOSINE REVEALS LINKS TO MITOCHRONDRIAL FUNCTION. Microbiology. 155: 3134-3141.
    
  • DISSECTING COLONY DEVELOPMENT OF NEUROSPORA CRASSA USING mRNA PROFILING AND COMPARTATIVE GENOMICS APPROACHES-(Peer Reviewed Journal)
    Kasuga, T., Glass, N.L. 2008. DISSECTING COLONY DEVELOPMENT OF NEUROSPORA CRASSA USING mRNA PROFILING AND COMPARTATIVE GENOMICS APPROACHES. Eukaryotic Cell. Vol. 7, No. 9, pp1549-1564.
    

• Projects

  Stacking RNAi-based Resistance to Phytophthora, Crown Gall, and Nematodes in Almond and Walnut Rootstocks Cooperative Agreement (A)   Accession Number:443615

  Improved Pest and Disease Control for Enhanced Woody Perennial Tree Crop and Grapevine Production In-House Appropriated (D)   Accession Number:441857

  Stacking RNAi-based Resistance to Phytophthora, Crown Gall, and Nematodes in Almond and Walnut Rootstocks Reimbursable Cooperative Agreement (R)   Accession Number:441580

  Development of RNA Interference-based Resistance in Almond and Walnut Rootstocks Against Phytophthora Pathogens Non-Assistance Cooperative Agreement (S)   Accession Number:438452

Research Program:

Dr. Kasuga's research is focused on the molecular genetics of Phytophthora ramorum, the causal agent of Sudden Oak Death. In recent years in California alone, over a million oak trees have been killed by P. ramorum. The pathogen also infects ornamentals, which serve as an inoculum source and means of spread to forest ecosystems. Due to its significance, a genome sequence of the pathogen was published in 2006. Taking full advantage of the genome data, his group conducts comparative genomics and transcriptomics, which will help us to decipher the mechanism of plant-P. ramorum interactions and to facilitate management of the pathogen.

Biography:

Dr. Takao Kasuga received his Bachelor of Engineering and Master of Engineering from Waseda University in Japan. Then he went to Scotland and received his Ph.D. in Genetics from Aberdeen University in 1995. His dissertation research investigated the population structures of forest pathogens Cronartium flaccidum and Heterobasidion annosum. Dr. Kasuga went on to a postdoctoral position in the Samuel Roberts Noble Foundation, Ardmore, Oklahoma with Dr. Madan Bhattacharyya, where he was involved in a project to isolate Phytophthora resistance genes in soybean. He then moved to Roche Molecular Systems, Alameda, California, where he studied biogeography of human pathogenic fungus Histoplasma capsulatum with Dr. Thomas White. For the past 6 years, he has been studying fungal development and evolution, at UC Berkeley, with Dr. Louise Glass and Dr. John Taylor, by means of microarray transcriptomics. In 2008, Dr. Kasuga joined the USDA-ARS in Davis, CA.