Sequencing and characterization of the Del/Tekay chromovirus family in Marshallia obovata (Asteraceae)

Abstract

Low coverage DNA sequencing data coupled with improved assembly methods are providing new insight into the repetitive fraction of the genomes of non-model organisms. In this study we explore the potential of these new approaches to characterize the Del/Tekay elements (chromodomain-containing Ty3/Gypsy retrotransposons) of the North American wildflower species Marshallia obovata. The Marshallia Del/Tekay chromoviruses are 8.3 Kbp in length with direct repeats of 1675 bp and 14 conserved domains across a 4506 bp gag-pol region. Read depth comparisons suggest that Del/Tekay elements are not highly abundant in M. obovata with approximately 144 unique copies per haploid genome of 6.5 Gbp (<0.02 %). Sequence variation was observed at less than 1 % of nucleotide positions overall with 60 % of variants occurring outside of any coding region. These results illustrate the utility of low coverage sequencing data for fine scale analyses of transposable elements present at low to moderate copy numbers within the genomes of non-model organisms. The Del/Tekay element sequences described here are the first for the plant family Asteraceae and are the first transposable elements of any kind described for the genus Marshallia. These initial results provide for future work on the evolutionary dynamics of Del/Tekay elements more broadly in the genus Marshallia and Asteraceae.