Download PAG XXIV San Diego 2016 Duckweeds, the smallest flowering

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
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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.
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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
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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
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• 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.
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