Hyunjin Koo
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
Authors
Soomin Kim
Hyun-Seung Park
Sang-Ji Lee
Nam-Chon Paek
Dr Jungnam Cho jungnam.cho@durham.ac.uk
Associate Professor
Tae-Jin Yang
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 |
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