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      Plant adaptive radiation mediated by polyploid plasticity in transcriptomes

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          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.

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          Most cited references 49

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          The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana.

          To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 x 10(-9) base substitutions per site per generation, the majority of which are G:C-->A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light-induced mutagenesis.
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            Ecological Speciation

             Patrik Nosil (2012)
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              Genome plasticity a key factor in the success of polyploid wheat under domestication.

              Wheat was domesticated about 10,000 years ago and has since spread worldwide to become one of the major crops. Its adaptability to diverse environments and end uses is surprising given the diversity bottlenecks expected from recent domestication and polyploid speciation events. Wheat compensates for these bottlenecks by capturing part of the genetic diversity of its progenitors and by generating new diversity at a relatively fast pace. Frequent gene deletions and disruptions generated by a fast replacement rate of repetitive sequences are buffered by the polyploid nature of wheat, resulting in subtle dosage effects on which selection can operate.
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                Author and article information

                Journal
                Molecular Ecology
                Mol Ecol
                Wiley
                09621083
                January 2017
                January 2017
                August 26 2016
                : 26
                : 1
                : 193-207
                Affiliations
                [1 ]Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
                [2 ]PRESTO; Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
                [3 ]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
                [4 ]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
                [5 ]Center for Ecological Research; Kyoto University; Hirano 2-509-3 Otsu 520-2113 Japan
                [6 ]Artificial Intelligence Research Center; AIST; 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
                [7 ]Kihara Institute for Biological Research; Yokohama City University; 641-12 Maioka, Totsuka-ward Yokohama Kanagawa 244-0813 Japan
                Article
                10.1111/mec.13738
                27352992
                © 2016

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