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Adaptation and speciation: evolutionary genomic analysis using arabidopsis relatives

English title Adaptation and speciation: evolutionary genomic analysis using arabidopsis relatives
Applicant Shimizu Kentaro
Number 116376
Funding scheme Project funding (Div. I-III)
Research institution Institut für Pflanzen- und Mikrobiologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Ecology
Start/End 01.04.2008 - 31.03.2011
Approved amount 340'015.00
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All Disciplines (2)

Discipline
Ecology
Genetics

Keywords (5)

adaptation; speciation; microarray; molecular genetics; arabidopsis

Lay Summary (English)

Lead
Lay summary
Millions species are living on the earth with astonishing diversity. Darwin proposed the first conclusive theory to explain organismal diversity with two principles: adaptation by natural selection, and speciation. However, little is known about the molecular mechanisms responsible for the diversity. The key to interdisciplinary study of biodiversity is evolutionary genomics (reviewed by Shimizu and Purugganan, Plant Phys. 2005). The basic data of evolutionary genomics is genomic information of multiple individuals of a species. Using such information, evolutionary genomics integrates ecology and molecular genetics in both directions. First, ecologically relevant genes can be identified by linkage disequilibrium (LD) mapping, quantitative trait locus (QTL) mapping, microarray or comparative genomics. Second, the adaptive meaning of a trait in nature can be shown by population genomic analysis. Adaptive evolution is the change of genomic constitution of the next generation due to survival and reproduction, and it leaves the molecular signatures of natural selection. To address questions on adaptation and speciation, we will use the model plant Arabidopsis thaliana and its relatives, which has enormous amount of genomic and genetic information available, and its relatives.This proposal will contribute to two fundamental and broad questions in evolutionary biology: which genes are responsible for adaptation and for speciation? What evolutionary processes affect allele frequency of these genes? Our website is:http://botserv1.uzh.ch/home/shimizu/index.html
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
The Cardamine hirsuta genome offers insight into the evolution of morphological diversity
Gan Xiangchao, Hay Angela, Kwantes Michiel, Haberer Georg, Hallab Asis, Ioio Raffaele Dello, Hofhuis Hugo, Pieper Bjorn, Cartolano Maria, Neumann Ulla, Nikolov Lachezar A., Song Baoxing, Hajheidari Mohsen, Briskine Roman, Kougioumoutzi Evangelia, Vlad Daniela, Broholm Suvi, Hein Jotun, Meksem Khalid, Lightfoot David, Shimizu Kentaro K., Shimizu-Inatsugi Rie, Imprialou Martha, Kudrna David, et al. (2016), The Cardamine hirsuta genome offers insight into the evolution of morphological diversity, in Nature Plants, 2(11), 16167-16167.
In Situ Enzyme Activity in the Dissolved and Particulate Fraction of the Fluid from Four Pitcher Plant Species of the Genus Nepenthes
Takeuchi Yayoi, Salcher Michaela M., Ushio Masayuki, Shimizu-Inatsugi Rie, Kobayashi Masaki J., Diway Bibian, von Mering Christian, Pernthaler Jakob, Shimizu Kentaro K. (2011), In Situ Enzyme Activity in the Dissolved and Particulate Fraction of the Fluid from Four Pitcher Plant Species of the Genus Nepenthes, in PLoS ONE, 6(9), e25144-e25144.
Plant flowering and sexual reproduction during climate change: quantitative prediction by eco-systems biology
Shimizu-Inatsugi Rie, Shimizu Kentaro K (2011), Plant flowering and sexual reproduction during climate change: quantitative prediction by eco-systems biology, in Cell Technology, 30, 167-173.
Single-Pollen Genotyping
Takeuchi Yayoi, Shimizu Kentaro K. (2011), Single-Pollen Genotyping, Springer Japan, Tokyo.
Using knockout mutants to reveal the growth costs of defensive traits
Zust T., Joseph B., Shimizu K. K., Kliebenstein D. J., Turnbull L. A. (2011), Using knockout mutants to reveal the growth costs of defensive traits, in Proceedings of the Royal Society B: Biological Sciences, 278(1718), 2598-2603.
Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene
Tsuchimatsu Takashi, Suwabe Keita, Shimizu-Inatsugi Rie, Isokawa Sachiyo, Pavlidis Pavlos, Städler Thomas, Suzuki Go, Takayama Seiji, Watanabe Masao, Shimizu Kentaro K. (2010), Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene, in Nature, 464(7293), 1342-1346.
Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment
Aikawa S., Kobayashi M. J., Satake A., Shimizu K. K., Kudoh H. (2010), Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment, in Proceedings of the National Academy of Sciences, 107(25), 11632-11637.
The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri
SHIMIZU-INATSUGI RIE, LIHOVÁ JUDITA, IWANAGA HIROKO, KUDOH HIROSHI, MARHOLD KAROL, SAVOLAINEN OUTI, WATANABE KUNIAKI, YAKUBOV VALENTIN V., SHIMIZU KENTARO K. (2009), The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri, in Molecular Ecology, 18(19), 4024-4048.
Evolution and Control of Imprinted FWA Genes in the Genus Arabidopsis
Fujimoto Ryo, Kinoshita Yuki, Kawabe Akira, Kinoshita Tetsu, Takashima Kazuya, Nordborg Magnus, Nasrallah Mikhail E., Shimizu Kentaro K., Kudoh Hiroshi, Kakutani Tetsuji (2008), Evolution and Control of Imprinted FWA Genes in the Genus Arabidopsis, in PLoS Genetics, 4(4), e1000048-e1000048.
Independent origins of self-compatibility in Arabidopsis thalianaSELF-COMPATIBILITY OF ARABIDOPSIS THALIANA
SHIMIZU KENTARO K., SHIMIZU-INATSUGI RIE, TSUCHIMATSU TAKASHI, PURUGGANAN MICHAEL D. (2008), Independent origins of self-compatibility in Arabidopsis thalianaSELF-COMPATIBILITY OF ARABIDOPSIS THALIANA, in Molecular Ecology, 17(2), 704-714.
MAA3 (MAGATAMA3) Helicase Gene is Required for Female Gametophyte Development and Pollen Tube Guidance in Arabidopsis thaliana
Shimizu K. K., Ito T., Ishiguro S., Okada K. (2008), MAA3 (MAGATAMA3) Helicase Gene is Required for Female Gametophyte Development and Pollen Tube Guidance in Arabidopsis thaliana, in Plant and Cell Physiology, 49(10), 1478-1483.

Awards

Title Year
Walter M. Fitch Prize for young investigators of the Society of Molecular Biology and Evolution (for the first time for a Swiss University) 2010

Associated projects

Number Title Start Funding scheme
135717 Evolution of breeding systems and phenology: evolutionary genomic analysis using Arabidopsis relatives 01.04.2011 Project funding (Div. I-III)

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