The Unique Composition of Transposons in the Basal Dicot Sacred Lotus

Transposable elements (TEs) are pervasive among eukaryotes and are often the largest component in these genomes. Their composition reflects the interaction between TEs and their host genomes, as well as the consequence of vertical inheritance and horizontal transfer. Sacred lotus, an ancient eudicot, represents the sister lineage to all core eudicots, and provides a unique reference for studying the evolution of dicots and the split between monocots and dicots. The sequencing of the sacred lotus genome has allowed us to characterize its repetitive content. Here, we report that 63% of the genome is composed of repetitive sequences, and the majority of them (55% of the genome) are identifiable TEs. Analysis of the TE content and diversity in sacred lotus revealed unique composition of TEs compared to other plant genomes characterized so far. Among LTR elements, a considerable portion (15%) are associated with non-canonical LTR ends which has not been reported for any other organisms. The detection of thousands of LTR elements with non-canonical ends suggests the long-term co-evolution between integrase and the termini of the element, providing new guideline for future annotation of LTR elements. Sacred lotus also contains the highest coverage and copy number of hAT elements among all genomes sequenced to date. The hAT elements make up a substantial portion (9%) of the genome, which may have favored the generation of novel domesticated hAT genes. In addition, the genome contains 1447 Pack-MULEs and provides the first evidence for the acquisition preference of GC-rich sequences by Pack-MULEs outside monocots.