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Transcriptomic analysis of polyploid species using second generation sequencers: how are they tolerant of broader range of environmental stresses?

Applicant Shimizu-Inatsugi Rie
Number 134200
Funding scheme Marie Heim-Voegtlin grants
Research institution Institut für Evolutionsbiologie und Umweltwissenschaften Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Genetics
Start/End 01.02.2011 - 31.01.2013
Approved amount 242'990.00
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All Disciplines (4)

Discipline
Genetics
Ecology
Botany
Molecular Biology

Keywords (4)

allopolyploid; homeolog gene; transcriptomics; next generation sequencer

Lay Summary (English)

Lead
Genome duplication could be one opportunity for the birth of new species. It is estimated that more than 70% plant species have experienced genome duplication in their history. However, very little is known about its molecular mechanism and the evolutionary and physiological significance. In this study, I focus on the gene expression control of allo- and auto-polyploid plant species, which have wider or different distribution and environmental tolerance compared to their parental species.
Lay summary
Genome duplication (polyploidization) could be one opportunity for the birth of new species, by combining either of the gene of the same species (autopolyploidization) or different species (allopolyploidization). It is estimated that more than 70% plant species have experienced genome duplication (polyploidization) in their history. There are several lines of evidence showing that polyploid speceis of plant are more adaptive for drastic environmental changes: Faucett et al (2009) showed that many angiosperm lineages have independently duplicated coincidentaly with the timing of the Cretaceous-Tertiary extinction event (65 million years ago) due to the advantage of altered gene expression leading to hybrid vigor and an increased set of genes. Polyploid species found in natural field tend to live in extreme habitat like cold arctic regions or dry habitat in Mediterranean climate. The theoretical researches for the last decades have revealed that it would be benefitial if some functional genes are duplicated (see Edger and Pires 2009 for review). In addition, high yield agricultural species tend to be polyploid. This fact suggests that genome duplication could have played a very important role in their evolutionary history of speciation or adaptation for new environments.
In spite of these facts, very little is known about the molecular mechanism to control the doubled genome, and the evolutionary and physiological significance of genome duplication. One of the main reasons is that most of polyploids are non-model species. Without any information about the genome sequence it was difficult to conduct molecular analysis, and even elucidating the parental species of allopolyploid species requires extensive effort in wild organisms.
In this study, I focus on the gene expression control of allo- and auto-polyploid plant species, which have wider or different distribution and environmental tolerance compared to their parental species. The analysis of wild species is enabled by taking advantage of two different types of 2nd generation sequencers. I hypothesize that a combination of two different sets of genes could be more adaptive for certain environment. The final goal is to give an answer to the question how polyploid species can be adaptive in such conditions. I use seven wild species (4 diploids, 2 allopolyploids and 1 autopolyploid) closely related to Arabidopsis thaliana, to exploit its genome information. The comparison of their expression patterns would reveal how two homeologs

Direct link to Lay Summary Last update: 15.03.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia.
Kubo Ken-ichi, Paape Timothy, Hatakeyama Masaomi, Entani Tetsuyuki, Takara Akie, Kajihara Kie, Tsukahara Mai, Shimizu-Inatsugi Rie, Shimizu Kentaro K, Takayama Seiji (2015), Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia., in Nature Plants, 1(14005), 1-9.
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis
Akama Satoru, Shimizu-Inatsugi Rie, Shimizu Kentaro K., Sese Jun (2014), Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis, in NUCLEIC ACIDS RESEARCH, 42(6), 46.
Speciation after the 20th century: adaptation to new environments by genome duplications.
Shimizu-Inatsugi Rie, Shimizu Kentaro K (2014), Speciation after the 20th century: adaptation to new environments by genome duplications., in Cell Technology (Saiboukougaku), 33(8), 878-883.
The More the Merrier: Recent Hybridization and Polyploidy in Cardamine
Mandakova Terezie, Kovarik Ales, Zozomova-Lihova Judita, Shimizu-Inatsugi Rie, Shimizu Kentaro K., Mummenhoff Klaus, Marhold Karol, Lysak Martin A. (2013), The More the Merrier: Recent Hybridization and Polyploidy in Cardamine, in PLANT CELL, 25(9), 3280-3295.
Chachapter 16: Genome duplication - speciation and ecogenomics of polyploid species.
Shimizu-Inatsugi Rie Shimizu Kentaro K (2012), Chachapter 16: Genome duplication - speciation and ecogenomics of polyploid species., in Morinaga Shinichi Kudoh Hiroshi (ed.), Kyoritsu, Tokyo, Japan, Tokyo, 246-262.
Quantified expression levels of genes in allopolyploid species.
Yamada Megumi, Shimizu-Inatsugi Rie, Shimizu Kentaro K, Sese Jun (2012), Quantified expression levels of genes in allopolyploid species., in IPSJ SIG Technical Reports, 21, 1-2.
Development of a microarrray for Fagus crenata (フナの DNA マイクロアレイの開発)
Saito Hideyuki, Sese Jun, Shimizu-Inatsugi Rie, Kamimura Shoko, Yamada Tadayasu, Shimizu Kenta (2011), Development of a microarrray for Fagus crenata (フナの DNA マイクロアレイの開発), in Forest Tree Breeding of Hokkaido, 54, 11-14.
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), 25144-25144.
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(2), 167-173.

Collaboration

Group / person Country
Types of collaboration
Slovak Academy of Sciences Slovakia (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Tsukuba University Japan (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Kyoto University Japan (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Tokyo Institute of Technology Japan (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Max Planck Institute, Cologne Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Nagoya University Japan (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Masaryk University Czech Republic (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Kyoto - Zurich Plant Workshop “Analyzing Plants in Complex Environments” Talk given at a conference Adaptation of allopolyploid species to new habitats 23.12.2014 Kyoto, Japan Shimizu-Inatsugi Rie;
SWISSPLANTS`12 Poster Transcriptomics of non-model polyploid plants with 2nd generation sequencers 18.01.2012 Meiringen, Switzerland, Switzerland Shimizu-Inatsugi Rie;
URPP Systems Biology/Functional Genomics Meeting 2011 Poster Transcriptomics od non-model polyploidy plants with 2nd generation sequencers 02.10.2011 Grindelwald, Switzerland, Switzerland Shimizu-Inatsugi Rie;
4th Retreat of the Institute of Plant Biology University of Zürich Talk given at a conference Allopolyploidization and adptive radiation of genus Cardamine 26.09.2011 Vitznau, Switzerland, Switzerland Shimizu-Inatsugi Rie;
Th 52th Annual Meeting of Japanese Society of Plant Physiologist Talk given at a conference Expresion studies of Arabidopsis relatives using Arabidopsis microarray 22.03.2011 Sendai, Japan Shimizu-Inatsugi Rie;


Knowledge transfer events



Self-organised

Title Date Place
Guided tour of the laboratory and botanical garden for children of Japanese primary and middle schools at Uster, Zurich 11.06.2012 Uster, Switzerland, Switzerland
Guided tour of the Botanical Garden of university of Zurich for Swiss-Japan association and Japan Club Zurich 13.05.2012 Zurich, Switzerland

Associated projects

Number Title Start Funding scheme
158542 PSC Discovery Program for Youth 01.04.2015 Agora

Abstract

Genome duplication is a common phenomenon in animals, fungi and plants. However, in spite of the fact that it played an important role in evolutionary history, very little is known about the molecular mechanism to control the doubled genome, and the evolutionary and physiological significance of genome duplication. In this study, I focus on the gene expression control of polyploid plant species, which have wider or different distribution and environmental tolerance compared to their parental species. The analysis of wild species is enabled by taking advantage of two different types of 2nd generation sequencers. I use seven wild species (4 diploids, 2 allopolyploids and 1 autopolyploid) closely related to Arabidopsis thaliana, to exploit its genome information I hypothesize that a combination of two sets of genes could be more adaptive for certain environments. In addition, I hope to find out new functional genes which play important roles for environmental tolerances.
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