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.
摘要：
长末端重复反转录转座子(LTR-RT)构成植物基因组的相当大一部分。这些活性LTR-RTs的新插入修饰了基因结构和功能，并在基因组进化中起着重要作用。因此,鉴定LTR-RTs的活性形式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eclDNA的LTR，然后测序（ALE-seq）揭示了LTR-RT的当前易位电位。通过在Nipponbare品种的愈伤组织中鉴定Tos17来验证ALE-seq方案。这里,基于ALE-seq技术，我们在水稻品种Dongjin愈伤组织中的6号和9号染色体上鉴定了属于Oryco家族的两个活性LTR-RT。每个Oryco家族成员具有具有相同序列和内部结构域区的配对LTR。两个LTR-RT的比较揭示了它们的内部结构域中97%的序列同一性和它们的LTR中65%的序列同一性。这两个假定具有活性的OrycoLTR-RT家族成员可用于扩展我们对逆转转座机制以及LTR-RT对水稻基因组的影响的了解。
