Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin

Koo, Hyunjin; Kim, Soomin; Park, Hyun-Seung; Lee, Sang-Ji; Paek, Nam-Chon; Cho, Jungnam; Yang, Tae-Jin

Abstract

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. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, amplification LTRs of eclDNAs followed by sequencing (ALE-seq) uncover the current transpositional potential of the LTR-RTs. The ALE-seq protocol was validated by identification of Tos17 in callus of Nipponbare cultivar. Here, we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in rice cultivar Dongjin callus based on the ALE-seq technology. 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. 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.

Citation

Koo, H., Kim, S., Park, H., Lee, S., Paek, N., Cho, J., & Yang, T. (2022). Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin. Mobile DNA, 13(1), Article 18. https://doi.org/10.1186/s13100-022-00274-2

• Journal Article Type: Article
• Acceptance Date: May 27, 2022
• Online Publication Date: Jun 13, 2022
• Publication Date: 2022
• Deposit Date: Nov 21, 2023
• Journal: Mobile DNA
• Print ISSN: 1759-8753
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 13
• Issue: 1
• Article Number: 18
• DOI: https://doi.org/10.1186/s13100-022-00274-2
• Public URL: https://durham-repository.worktribe.com/output/1945376