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Browsing by Author "Boore, Jeffrey L."

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    Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana
    Radakovits, Randor; Jinkerson, Robert E.; Fuerstenberg, Susan I.; Tae, Hongseok; Settlage, Robert E.; Boore, Jeffrey L.; Posewitz, Matthew C. (Springer Nature, 2012-02)
    The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (similar to 29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.
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    Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
    Lévesque, C. A.; Brouwer, Henk; Cano, Liliana; Hamilton, John P.; Holt, Carson; Huitema, Edgar; Raffaele, Sylvain; Robideau, Gregg P.; Thines, Marco; Win, Joe; Zerillo, Marcelo M.; Beakes, Gordon W.; Boore, Jeffrey L.; Busam, Dana; Dumas, Bernard; Ferriera, Steve; Fuerstenberg, Susan I.; Gachon, Claire M.; Gaulin, Elodie; Govers, Francine; Grenville-Briggs, Laura; Horner, Neil; Hostetler, Jessica; Jiang, Rays H.; Johnson, Justin; Krajaejun, Theerapong; Lin, Haining; Meijer, Harold J.; Moore, Barry; Morris, Paul; Phuntmart, Vipaporn; Puiu, Daniela; Shetty, Jyoti; Stajich, Jason E.; Tripathy, Sucheta; Wawra, Stephan; van West, Pieter; Whitty, Brett R.; Coutinho, Pedro M.; Henrissat, Bernard; Martin, Frank; Thomas, Paul D.; Tyler, Brett M.; De Vries, Ronald P.; Kamoun, Sophien; Yandell, Mark; Tisserat, Ned; Buell, C. Robin (2010-07-13)
    Background Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans. Conclusions Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.