Patterns of polymorphism, selection and linkage disequilibrium in the subgenomes of the allopolyploid Arabidopsis kamchatica
Dr. Timothy Paape, Roman Briskine, Heidi Lischer, Gwyneth Halstead-Nussloch, Rie Shimizu-Inatsugi, Masaomi Hatekayama, Kenta Tanaka, Dr. Tomoaki Nishiyama, Renat Sabirov, Jun Sese, Prof. Kentaro K Shimizu
Received: 16th January 18
Although genome duplication is widespread in wild and crop plants, little is known about genome-wide selection due to the complexity of polyploid genomes. In allopolyploid species, the patterns of purifying selection and adaptive substitutions would be affected by masking owing to duplicated genes or ‘homeologs’ as well as by effective population size. We resequenced 25 distribution-wide accessions of the allotetraploid Arabidopsis kamchatica, which has a relatively small genome size (450 Mb) derived from the diploid species A. halleri and A. lyrata. The level of nucleotide polymorphism and linkage disequilibrium decay were comparable to A. thaliana, indicating the feasibility of association studies. A reduction in purifying selection compared with parental species was observed. Interestingly, the proportion of adaptive substitutions (α) was significantly positive in contrast to the majority of plant species. A recurrent pattern observed in both frequency and divergence-based neutrality tests is that the genome-wide distributions of both subgenomes were similar, but the correlation between homeologous pairs was low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation.
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This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.