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

Mobile DNA

Jungnam Cho¹  Hyunjin Koo²  Sang-Ji Lee²  Nam-Chon Paek²  Hyun-Seung Park²  Tae-Jin Yang²  Soomin Kim² 

[1]CAS-JIC Centre of Excellence for Plant and Microbial Science

[2]Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University

关键词: Long terminal repeat retrotransposon;    Transposition;    ALE-seq;    Oryza sativa;    Dongjin;   

DOI  :  10.1186/s13100-022-00274-2

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown