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.
Highlights
Genome duplication is widespread in wild and crop plants
196,243,198 14.81 2239 932 4,302,264 712,249 71 489,153 117 250 Mb av2.2 of Siberian A. lyrata subsp. petraea assembled in this study bA. halleri assembly previously reported in Briskine et al.[38] cMissing data counted as number of Ns in the assembly and are a percentage of total length dGenome size measured by flow cytometry (FC)
Because most of these positions were represented by two homeologs of multiple A. kamchatica individuals, we counted a total of 1375 single-nucleotide polymorphisms (SNPs) sites
Summary
Genome duplication is widespread in wild and crop plants. little is known about genome-wide selection in polyploids due to the complexity of duplicated genomes. 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. 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. Divergence–diversity-based tests compare interspecific divergence (from an outgroup) with intraspecific polymorphism to identify positive selection on amino-acid substitutions[12] These tests include several derivatives of the McDonald–Kreitman test[13] (or MK tests), such as the DoS neutrality index[14], and methods to estimate the distribution of fitness effects (DFEs) and proportion of adaptive substitutions (α)[13] in genome-wide data. The high variation in latitude and altitude compared with the parental species[34,35] suggests that merging the diploid transcriptional networks and parental adaptations provided the allopolyploid with plasticity to inhabit diverse environments[10]
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