LTR Retrotransposons and TIR-flanked DNA Transposons Account for the Genome Expansion, Structure and Organization in the Palms

The coconut (Cocos nucifera) has been an important contributor to the Philippine economy. To elucidate the evolutionary processes that helped shaped its extant genome, and be able to further enlighten its varietal improvement and sustainability programs, we compared the repetitive element components of the different members of the palm family. Here we investigated the repeats in Elaeis guineensis (African oil palm), Elaeis oleifera (South American oil palm), Phoenix dactylifera (date palm) and coconut and analyzed how their genomes were formed by transposition of transposable elements. Of these palm family members, coconut possesses the largest genome size (~2.9 Gb) and our preliminary results suggest that this expansion is largely attributed to LTR retrotransposons and TIR-flanked DNA transposons. It is estimated that the palm common ancestor lived about 65 million years ago (Mya) and that coconut was the first to split which occurred just shortly after 65 Mya. Interestingly, a significantly huge Copia and Gypsy burst in coconut ensued at ~3.6 Mya accounting for approximately 19% of the sequence dataset. This activity was relatively recent in coconut compared to the other palms and greatly expanded the genome. The CACTA-EnSpm superfamily trails in abundance and given that this superfamily is generally associated with genes and genic regions, we hypothesize that these elements, along with the Copia and Gypsy retrotransposons significantly contributed to the genome structure and organization of coconut.