Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica.

Autor: Paape T; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland. tim.paape@ieu.uzh.ch.; Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland. tim.paape@ieu.uzh.ch., Briskine RV; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.; Department of Environmental Systems Science, ETH Zurich, CH-8092, Zurich, Switzerland.; Functional Genomics Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland., Halstead-Nussloch G; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland., Lischer HEL; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.; Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland., Shimizu-Inatsugi R; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.; Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland., Hatakeyama M; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.; Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland.; Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland.; Functional Genomics Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland., Tanaka K; Sugadaira Montane Research Center, University of Tsukuba, Nagano, Ueda, 386-2204, Japan., Nishiyama T; Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan., Sabirov R; Institute of Marine Geology and Geophysics, Far East Branch, Russian Academy of Sciences, Nauki street, 1-B, Yuzhno-Sakhalinsk, 693022, Russian Federation., Sese J; Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan.; AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory, Tokyo, 152-8550, Japan., Shimizu KK; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland. kentaro.shimizu@ieu.uzh.ch.; Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland. kentaro.shimizu@ieu.uzh.ch.; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Yokohama, 244-0813, Japan. kentaro.shimizu@ieu.uzh.ch.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2018 Sep 25; Vol. 9 (1), pp. 3909. Date of Electronic Publication: 2018 Sep 25.
DOI: 10.1038/s41467-018-06108-1
Abstrakt: Genome duplication is widespread in wild and crop plants. However, little is known about genome-wide selection in polyploids due to the complexity of duplicated genomes. In polyploids, the patterns of purifying selection and adaptive substitutions may be affected by masking owing to duplicated genes or homeologs as well as effective population size. Here, we resequence 25 accessions of the allotetraploid Arabidopsis kamchatica, which is derived from the diploid species A. halleri and A. lyrata. We observe a reduction in purifying selection compared with the parental species. Interestingly, proportions of adaptive non-synonymous substitutions are significantly positive in contrast to most plant species. A recurrent pattern observed in both frequency and divergence-diversity neutrality tests is that the genome-wide distributions of both subgenomes are similar, but the correlation between homeologous pairs is low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation.
Databáze: MEDLINE
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