Towards Understanding the Evolution of Repeat Elements in Caryophyllales

Genome sequences of species under the plant order Caryophyllales are underrepresented in the copious plant genome sequencing efforts. As a result, in the publicly available databases of known repeats such as RepBase and that from mips-RE-dat, Caryophyllales-specific repeats are also underrepresented. In the work presented here, we have taken advantage of the draft genome sequence of Amaranthus hypochondriacus, sequenced and assembled in-house, and the recently published genome of Beta vulgaris to discover and characterize Caryophyllales-specific repeats.  We have used both homology-based and de novo prediction tools to discover repeats in both these species and have used RepeatMasker to estimate the repeat content in their respective genomes. Masking the genomes using the predicted repeats from the respective genomes using RepeatScout revealed significantly lower percentage of repeats in A. hypochondriacus genome compared to other plant species. A more rigorous prediction of repeats using RepeatModeler masked only 13.76% of A. hypochondriacus genome, still far below the 63% reported for B. vulgaris. The lower percentage of repeats in A. hypochondriacus genome may suggest that either amaranth specific repeats have diverged from those of other species represented in Repbase or that B. vulgaris has been under the influence of active evolution after speciation. The lower repeat content in A. hypochondriacus is further validated using C₀t analysis and will be presented.