Characterization Of Transposable Elements In The Ancestral Angiosperm Amborella trichopoda

Amborella trichopoda is an understory shrub that is the sister species to all extant Angiosperms and thus represents an important reference genome for the study of the evolutionary genomics of flowering plants. The Amborella nuclear genome has been sequenced using a whole genome shotgun strategy and assembled into 5,745 scaffolds totaling 706 Mb. We have used the DAWGPAWS, RepMiner, and TARGET analysis pipelines to generate a comprehensive annotation and classification of the transposable elements in this important reference genome. The TE insertions in Amborella are generally 2 to 4 times as old as those found in previously described plant genomes, and the detectable TEs and repeats comprise over 58% of the genome assembly. Helitrons, hAT, PIF/Harbinger, and Mutator DNA transposons were all discovered to be present in the assembled genome, while the CACTA and TC1/Mariner superfamilies were not detected. Both Gypsy and Copia LTR retrotransposon were found in high copy number, as were the L1 and RTE LINE non-LTR retrotransposons. Endogenous Pararetroviruses (EPRVs) also significantly contribute to the repeat landscape and comprise almost 3% of genome scaffold sequences. MITEs were also found to be in high copy number throughout the Amborella genome, although the ancient age of DNA transposon insertions and the subsequent degradation of TIR sequences made it difficult to assign relationships between MITEs and their autonomous partners.