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Abstract

In plants, a common mechanism through which genome size is drastically altered and genome evolution is rapidly altered is whole genome duplication (WGD), or polyploidization. WGDs are strikingly common transitions, having occurred sometime in the histories of all flowering plant species, and often re-occur within single lineages. While a WGD will result in an instant doubling of genome size, both the subsequent rediploidization process and the potential for an increase in transposable element (TE) activity after the event means that past WGDs can be cryptic in current diploid lineages, and can potentially cause substantial variation in genome size. Genomic evidence for the role of WGDs in driving genome size variation and an increase in TE activity, however, has been limited by the lack of comparative genomic datasets which include variation in WGD history. In order to better understand the role of WGD in genome evolution, we sequenced and assembled 19 new genomes in the Brassicales, doubling the current available genomes for the family, to provide 32 species containing 9 independent WGD events. Using this comparative genomic data, we show that 81% of the variation in genome size across the family can be explained by past WGD events and TE content. We further show that WGDs caused bursts of TE activity, and largely explain current TE abundance, with evidence for relaxed selection after WGD events leading to genome wide relaxed selection against TEs inserting near conserved regions. Finally, we provide evidence for both gain and loss of conserved noncoding elements following WGD, consistent with relaxed genome wide selection and functional redundancy driving the evolution of normally static sequence.