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

IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Mobile DNA Pub Date : 2022-06-13 DOI:10.1186/s13100-022-00274-2
Koo, Hyunjin, Kim, Soomin, Park, Hyun-Seung, Lee, Sang-Ji, Paek, Nam-Chon, Cho, Jungnam, Yang, Tae-Jin
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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.
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染色体外线性dna LTRs扩增(ALE-seq)鉴定了两个活性Oryco LTR反转录转座子
长末端重复反转录转座子(LTR-RTs)在植物基因组中占相当大的比例。这些活性LTR-RTs的新插入修饰了基因结构和功能,并在基因组进化中发挥重要作用。因此,鉴定活性形式的LTR-RTs可以揭示这些元素在植物中的作用。染色体外线性DNA (eclDNA)在LTR-RT复制过程中形成;因此,扩增eclnas的ltr并进行测序(ALE-seq)可以揭示LTR-RTs当前的转位潜力。通过对日本品种愈伤组织中Tos17的鉴定,验证了ALE-seq方法的有效性。本研究利用ALE-seq技术,在水稻品种东津愈伤组织的6号和9号染色体上鉴定了两个Oryco家族的活性LTR-RTs。每个Oryco家族成员都有具有相同序列和内部结构域的配对ltr。两个LTR-RTs的比较显示,其内部结构域的序列一致性为97%,ltr的序列一致性为65%。这两个推测活跃的Oryco LTR-RT家族成员可以用来扩展我们对水稻基因组逆转录转位机制和LTR-RT影响的认识。
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来源期刊
Mobile DNA
Mobile DNA GENETICS & HEREDITY-
CiteScore
8.20
自引率
6.10%
发文量
26
审稿时长
11 weeks
期刊介绍: Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.
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