Repeatability of Gene Loss in Polyploid Arabidopsis kamchatica

Polyploidization of Arabidopsis kamchatica (AK) from diploid Arabidopsis halleri (AH) and Arabidopsis lyrata (AL) resulted in immediate duplication of thousands of genes. While some genes were lost in the initial chaotic restructuring, others were subsequently lost over thousands of years through stochastic mutagenesis caused by genetic redundancy. Using genome sequences from their parental references, hundreds of genes were found to be lost in AK. Gene homeologs that were lost in AK typically had low sequence divergence between parental AH and AL lines, while having high within-species polymorphism within their parental lineages. These genes were also found to be away from network hubs, exhibiting less centrality and connectivity. Genes from AL were more likely to be lost, and exhibited less positive selection than homeologs from AH. The preferential retention of AH homeologs may reflect the current geographical distribution of AK in an area dominated by AH.