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

Timothy Paape (), Roman V. Briskine, Gwyneth Halstead-Nussloch, Heidi E. L. Lischer, Rie Shimizu-Inatsugi, Masaomi Hatakeyama, Kenta Tanaka, Tomoaki Nishiyama, Renat Sabirov, Jun Sese and Kentaro K. Shimizu ()
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Timothy Paape: University of Zurich
Roman V. Briskine: University of Zurich
Gwyneth Halstead-Nussloch: University of Zurich
Heidi E. L. Lischer: University of Zurich
Rie Shimizu-Inatsugi: University of Zurich
Masaomi Hatakeyama: University of Zurich
Kenta Tanaka: University of Tsukuba
Tomoaki Nishiyama: Kanazawa University
Renat Sabirov: Institute of Marine Geology and Geophysics, Far East Branch, Russian Academy of Sciences
Jun Sese: Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST)
Kentaro K. Shimizu: University of Zurich

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: Abstract 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.

Date: 2018
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DOI: 10.1038/s41467-018-06108-1

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