title: Plant adaptive radiation mediated by polyploid plasticity in transcriptomes.
abstract: The habitats of polyploid species are generally distinct from their parental species. Stebbins described polyploids as 'general purpose genotypes', which can tolerate a wide range of environmental conditions. However, little is known about its molecular basis because of the complexity of polyploid genomes. We hypothesized that allopolyploid species might utilize the expression patterns of both parents depending on environments (polyploid plasticity hypothesis). We focused on hydrological niche segregation along fine-scale soil moisture and waterlogging gradients. Two diploid species, Cardamine amara and Cardamine hirsuta, grew best in submerged and unsubmerged conditions, respectively, consistent with their natural habitats. Interestingly, the allotetraploid Cardamine flexuosa derived from them grew similarly in fluctuating as well as submerged and unsubmerged conditions, consistent with its wide environmental tolerance. A similar pattern was found in another species trio: allotetraploid Cardamine scutata and its parents. Using the close relatedness of Cardamine and Arabidopsis, we quantified genomewide expression patterns following dry and wet treatments using an Arabidopsis microarray. Hierarchical clustering analysis revealed that the expression pattern of C. flexuosa clustered with C. hirsuta in the dry condition and with C. amara in the wet condition, supporting our hypothesis. Furthermore, the induction levels of most genes in the allopolyploid were lower than in a specialist diploid species. This reflects a disadvantage of being allopolyploid arising from fixed heterozygosity. We propose that recurrent allopolyploid speciation along soil moisture and waterlogging gradients confers niche differentiation and reproductive isolation simultaneously and serves as a model for studying the molecular basis of ecological speciation and adaptive radiation.
authors.affiliation: Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
authors.forename: Rie
authors.initials: R
authors.lastname: Shimizu-Inatsugi
authors.affiliation: PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.|Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.|Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
authors.forename: Aika
authors.initials: A
authors.lastname: Terada
authors.affiliation: Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan.
authors.forename: Kyosuke
authors.initials: K
authors.lastname: Hirose
authors.affiliation: Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kudoh
authors.affiliation: Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.|Artificial Intelligence Research Center, AIST, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Sese
authors.affiliation: Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.|Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.|Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan.|Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, Kanagawa, 244-0813, Japan.
authors.forename: Kentaro K
authors.initials: KK
authors.lastname: Shimizu
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D031217:Cardamine / Q000145:classification*; D004171:Diploidy; D017753:Ecosystem; D011123:Polyploidy; D060047:Reproductive Isolation; D059467:Transcriptome; D014867:Water
chemical_list: D014867:Water
keywords: advantages and disadvantages of polyploidization; ecological speciation; generalist; genome duplication; specialist; water-usage gradients