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Amborella Genome Projects: Challenges and Opportunities for Applying Ontologies

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Amborella Genome Projects: Challenges and Opportunities for Applying Ontologies The Floral Genome/AncestralAngiosperm/Amborella Genome Projects: Challenges and opportunities for applying ontologies Claude dePamphilis Penn State University PAG Plant Ontology 10:55 AM, Hamilton http://www.floralgenome.org/ http://www.ancangio.uga.edu/ http://www.amborella.org/ Photo: Sangtae Kim Diversity of floral structure in early angiosperms Amborella trichopoda Nuphar advena Persea americana Photo: Sangtae Kim Yellow spatterdock Avocado Photo: Yi Hu Liriodendron tulipifera Aristolochia fimbriata Zamia vazquezii Yellow poplar Birthwort Cycad Photo: Yi Hu Photo: Mauro Peixoto Photo: D. Stevenson The Floral Genome Project 2001-2007 Objectives: • Investigating the origin, conservation, and diversification of the genetic architecture of the flower • Developing conceptual and real tools for evolutionary functional genomics in plants Key Questions: • How much of the knowledge on floral development from model transferrable to other systems? • What is the “common toolbox” for a critical developmental process in plants? • How did the floral developmental program http://www.floralgenome.org/ originate and diversify? Tree Drawing: Joel R. McNeal Flowering Pathways GA Autonomous Vernalization LD Repression FCA FLD FPA VRN1 PHYA EMF1 The Expanding Flowering FY LD FVE VRN2 EMF2 Time GI Floral Genes FRI CO Integrating FLC Developmental Genes SOC FT TFL1 Network of Meristem Identity FUL Arabidopsis Genes AP2 LFY AP1 CAL Cadastral UFO WUS AP2 LUG Genes AG ASK1 SUP LSN SEU Organ AP1 AP2 AP3 PI SEP AG Identity Genes Flower Sepals Petals Stamens Carpels organs Photo: Yi Hu Reconstruction of LACA √ Flowers, Fruits, Double fertilization √ Flowers indeterminate or trimerous √ Perianth likely spiral (or whorled) √ Perianth undifferentiated into sepals, petals √ Carpels seal by secretion √ Woody √ Xylem lacked vessels √ They were dicots! Soltis et al., Phylogeny and Evolution of Angiosperms FGP PLANT SPECIES *Welwitschia BASAL ANGIOSPERMS: Zamia Amborella, Nuphar, Illicium, Amborella Persea, Liriodendron, Saruma *Nuphar star anise MONOCOTS: *P, L, S Acorus Acorus, Asparagus Oryza Oryza, Zea, palm *poppy Arabidopsis EUDICOTS: poppy (Eschscholzia), Mesembryanthemum, Vaccinium, Cucumis, Ribes Arabidopsis, Medicago, Populus, Beta, Lycopersicon, Antirrhinum, Malus, & others GYMNOSPERMS: Zamia, Welwitschia & Selaginella, Physcomitrella Pinus, Ginkgo, Gnetum Floral development studies (Matyas Buzgo) Stage 2: Sepal initiation Stage 3: Petal initiation Stage 4: Stamen initiation Stage 5: Carpel initiation Stage 6: Microsporangia initiation Stage 7: Ovule initiation Fading Borders Hypothesis (Buzgo, 2005) Medicago Lotus Malus (apple)Gycine Cucumis (cucumber) Eudicots Populus (poplar) Gossypium (cotton) (I) Monocots Citrus (orange) Brassicales B Magnoliids Vitis (grape) Ribes (currant) A C Antirrhinum 1st 2nd 3rd 4th Mimulus Solanaceae Asteraceae Vaccinium (blueberry) (II) Mesembryanthemum B Beta Eschscholzia Papaver (opium poppy) A C Aquilegia Poaceae 1st 2nd 3rd 4th Musa (I) Allium (onion)* Asparagus B Acorus Liriodendron Persea (avocado) A C Aristolochia 1st 2nd 3rd 4th Illicium Saruma (III) Nymphaea Nuphar A(?) Amborella B Cryptomeria Gymnosperms C Welwitschia 1st 2nd 3rd 4th Gnetum Pinus, Picea Ginkgo Cycas Zamia 2005. Biologist 52: 149 AAGP Sequencing (2007-2011) Homology of floral organs in basal angiosperms? Homology of floral organs in basal angiosperms? Environmental determination of petaloid tepals, including surface structures Mosaic Theory: petaloidy evolved in early angiosperms, but genetic determination came later Petal Microarrays (4-5 total) •Arabidopsis Anther (17-25 total) •Eschscholzia 2-4 whorls •Persea Pistil (1) •Nuphar Sepal (2 total) Leaf - 138 (67) Medium bud 14 (9) Sepal - 136 (47) Small bud Petal -125 (8) 103 (58) Fruit Stamen - 347 (107) 52 (12) Carpel - 22 (1) Laura Zahn, PSU / AAAS Large scale expression to “define” structures Chanderbali….P. Soltis, 2010. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. PNAS 107: 22570-5 Large scale expression to “define” structures Chanderbali….P. Soltis, 2010. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. PNAS 107: 22570-5 Polyploidy as a dominant process Jiao…..dePamphilis. 2011. Ancestral polyploidy in seed plants and angiosperms. Submitted Amborella Genome Sequencing (2011-2015) • Dioecious trees or shrubs… • Sister to all other angiosperms – a reference for angiosperm comparative genomics • Native only to New Caledonia, brought into “The transition from bracts to cultivation at UC Santa Cruz tepals is gradual, making it difficult to determine exactly • Vesselless; decussate and alternate phylotaxy; where a flower flowers spiral / whorled begins in this species.” • Gene Expression Atlas an added goal Buzgo et al IJPS 165: 925 Acknowledgements 1=FGP, 2=AAGP, 3=Ambo Barbara Bliss (1,2) PSU Vic Albert (1,3) Buffalo Matyas Buzgo (1) FLA Naomi Altman (1,2) PSU James Bremmer (3) UCR Brad Barbazuk (3) FLA Sam Brockington (1) FLA John Carlson (1) PSU Andre Chanderbali (1,2,3) FLA Sandra Clifton (2) WASH U Srikar Chamal (3) FLA Claude dePamphilis (1,2,3) PSU Liying Cui (1) PSU Josh Der (3) PSU Jill Duarte (1,2) PSU Mike Frohlich (1) KEW Jamie Estill (3) FLA Jim Leebens-Mack (1,2,3) UGA Wei Hu (1) PSU Hong Ma (1,2,3) PSU Yuannian Jiao (2,3) PSU David Oppenheimer (1) FLA Hongzhi Kong (1) PSU/CAS Steve Rounsley (3) AZ/Dow Sangtae Kim (1) FLA Stephan Schuster (2,3) PSU Raj S. (2,3) Doug Soltis (1,2,3) FLA Eric Wafula (3) PSU Pam Soltis (1,2,3) FLA Kerr Wall (1,2) PSU/BASF Steve Tanksley (1) CORNELL Brandon Waltz (3) PSU Sue Wessler (3) UCR Norm Wickett (2,3) PSU Rod Wing (2,3) AZ Mee-Jeoong Yoo (1,2) FLA Laura Zahn (1) PSU/AAAS Andrea Zuccolo (2) AZ THANK YOU! •NSF Plant Genome Research Program! •Our techs: Lena Landherr, Paula Ralph •Plant tissues and plant sharing: U.C. Santa Cruz (Amborella) Dennis Stevenson (Zamia), Jeannie Rowland (Vaccinium), Scott Schlarbaum (Liriodendron), Rafael Perl-Treves (Cucurbita), V. Irish (Papaver), K. Sink and M. Havey (Asparagus) Photo: Yi Hu.
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