In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae)
In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae)
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DOI：
10.1016/j.ympev.2021.107236
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发表时间：
2021-06-29
影响因子：
4.1
通讯作者：
Jansen, Robert K.
中科院分区：
文献类型：
--
作者：
Choi, In-Su;Wojciechowski, Martin F.;Jansen, Robert K.
植物特异性有丝分裂病毒属（Narnaviridae）的有丝分裂病毒及其整合序列（非逆转录病毒内源RNA病毒元件或NERVE）最近已在各种植物谱系中鉴定。然而，植物线粒体基因组（mitogenome）序列的稀疏系统发育覆盖率和线粒体基因间区域的非保守性阻碍了植物中的线粒体病毒NERVEs的比较研究。在这项研究中，10个新的有丝分裂基因组测序豆类（豆科）。基于对27个总有丝分裂基因组的比较基因组分析，我们鉴定了整个家族的有丝分裂病毒神经和转座因子。所有豆科植物有丝分裂基因组包括神经和总神经长度从约。在蝶形三叶草中为2kb，在含羞草金合欢中为35kb。大部分NERVE整合位点位于高度可变的基因间区域，然而，一些位于六个顺式剪接的线粒体内含子中。在金合欢有丝分裂基因组中，存在L1样转座子序列，包括具有靶位点重复（TSDs）的几乎全长拷贝。NERVE在4个内含子中的整合位点显示出L1样反转录转座事件的证据。系统发育分析显示，在TSD之间存在多个神经元精确缺失的实例。这项研究提供了明确的证据表明，L1样反转录转座机制具有悠久的历史，有助于病毒RNA整合到植物有丝分裂基因组中，而微同源介导的缺失可以恢复整合位点。
Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the nonconserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.