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1/19/2016 Duckweeds, the smallest flowering plants in the world The ancient genome of an aquatic plant, Spirodela polyrhiza, at the root of monocot evolution PAG XXIV San Diego 2016 Joachim Messing Waksman Institute Rutgers University New Jersey, USA Leaves and stems are merged into a common flattened ovoid structure called a frond or thallus, some species have thread-like rootlets Propagation occurs primarily by budding of new fronds The entire plant body is composed of metabolically active cells rather than structural, supportive tissues so the plants have twice the protein, fat, nitrogen and phosphorus of typical vascular plants Duckweeds comprise 5 genera and 38 species higher protein content than soybean (high Met & Lys content) high -carotene content used as fish, poultry, & livestock feed (humans consume “water meal” in Thailand) Phylogeny of duckweeds (Lemnoideae) Computational separation of genomes from total leaf DNA Chloroplast and mitochondrial genomes were rapidly evolving An Arabidopsis leaf cell: •100 copies of mtDNA •1,000 cpDNA •2 nuclear DNA SOLiD 5500XL Logan DC. J Exp Bot, 2006. Wang W, Messing J. PLoS One 2011. Wang W, Wu Y, Messing J. PLoS One 2012. 1 1/19/2016 Sequencing the Spirodela genome Sequence assembly and chromosomes •Newbler 2.6 assembly of shotgun reads • BAC ends to select 96 complete BACs •Multicolor FISH with BACs to reduce 32 pseudomolecules to 20 chromsomes •https://www.waksman.rutgers.edu/ spirodela/genome 454 FLX+ Cao et al. (2016) New Phytol. 209: 354:363 Wang et al. (2014) Nat Commun. 5:3311 3730XL Repetitive DNA content among angiosperms Gene families and genome evolution 19,623 protein-coding genes, 25% less than Arabidopsis, 50% less than rice A reduction of genes involved in cell wall biosynthesis and lignification An increase of repressors of the transition from juvenile to adult phase Two ancient rounds of whole-genome duplications No recent retrotranspositions Reduced gene copies for lignin Definition: Finding: Lignin, as a major component of secondary cell wall, plays an important role for up-straight structure in vascular plants. Increased gene copies for GOGAT Definition: Finding: Glutamine synthetase (GS) and glutamate synthase (GOGAT) are the core enzymes for N-assimilation. Arabidopsis Spirodela Lifestyle: Lifestyle: Fast growing requires N 2 1/19/2016 Highlights Gene network for juvenile growth Definition: • Duckweeds belong to the Lemnoideae and are the fastest growing plants on earth used in bioremediation and industrial applications. Neoteny is the retention of juvenile traits • Duckweeds belong to the order of Alismatales, which have diverged from other monocot species whose genomes have been sequenced. Finding: Enhancer is reduced Repressor is increased Arabidopsis Rice Spirodela Lifestyle: miRNA156 10 19 32 miRNA172 9 1 • The Spirodela genome is one of the smallest among monocots (157 MB) with two ancient WGDs and lack of recent transpositions. • The Spirodela genome has 25% less gene models than Arabidopsis and 50% less than rice. • The Spirodela genome has an expansion and contraction of gene families that correlate with its aquatic environment and neoteny. Vegetative growth by frond budding Spirodela genome sequencing consortium Mayer, K.F.X. Haberer, G. Grundlach, H. Gläßer, C. Nussbaumer, T. Messing, J Kerstetter, R.A. Michael, T.P. Wang, W. Fourounjian, P. Schmutz, J. Rokhsar, D. Adam, C Grimwood, J. Jenkins, J. Chow, J. Choi, C. Appenroth, K. Schubert, I. Cao,XH. Fuchs, J. Borodovsky, M. Lomsadze, A. Luo, M.-C. Mockler, T. Bryant D. Shanklin, J. 3