Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin

Background: Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants. Results: To identify active LTR-RTs in rice ( Oryza sativa ), we characterized 1,783 intact LTR-RTs in the rice reference genome. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, we amplified LTRs of eclDNA (ALE)-seq to uncover the current transpositional potential of the LTR-RTs in callus of the Korean rice variety Dongjin. Tos17 was discovered in callus of the reference rice variety Nipponbare, and we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in Dongjin callus. Each Oryco family member has paired LTRs with identical sequences and internal domain regions. Comparison of the two LTR-RTs revealed 97% sequence identity in their internal domains and 65% sequence identity in their LTRs. Conclusions: We identified two active LTR-RTs in the callus of Korean rice variety Dongjin using ALE-seq. These two putatively active Oryco LTR-RT family members could be used to expand our knowledge of retrotransposition mechanisms and the effects of LTR-RTs on the rice genome.