Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
PLoS Pathog. 2011 Jul;7(7):e1002146. doi: 10.1371/journal.ppat.1002146. Epub 2011 Jul 14.
Non-retroviral RNA virus sequences (NRVSs) have been found in the chromosomes of vertebrates and fungi, but not plants. Here we report similarly endogenized NRVSs derived from plus-, negative-, and double-stranded RNA viruses in plant chromosomes. These sequences were found by searching public genomic sequence databases, and, importantly, most NRVSs were subsequently detected by direct molecular analyses of plant DNAs. The most widespread NRVSs were related to the coat protein (CP) genes of the family Partitiviridae which have bisegmented dsRNA genomes, and included plant- and fungus-infecting members. The CP of a novel fungal virus (Rosellinia necatrix partitivirus 2, RnPV2) had the greatest sequence similarity to Arabidopsis thaliana ILR2, which is thought to regulate the activities of the phytohormone auxin, indole-3-acetic acid (IAA). Furthermore, partitivirus CP-like sequences much more closely related to plant partitiviruses than to RnPV2 were identified in a wide range of plant species. In addition, the nucleocapsid protein genes of cytorhabdoviruses and varicosaviruses were found in species of over 9 plant families, including Brassicaceae and Solanaceae. A replicase-like sequence of a betaflexivirus was identified in the cucumber genome. The pattern of occurrence of NRVSs and the phylogenetic analyses of NRVSs and related viruses indicate that multiple independent integrations into many plant lineages may have occurred. For example, one of the NRVSs was retained in Ar. thaliana but not in Ar. lyrata or other related Camelina species, whereas another NRVS displayed the reverse pattern. Our study has shown that single- and double-stranded RNA viral sequences are widespread in plant genomes, and shows the potential of genome integrated NRVSs to contribute to resolve unclear phylogenetic relationships of plant species.
非逆转录 RNA 病毒序列（NRVS）已在脊椎动物和真菌的染色体中被发现，但在植物中未被发现。在此，我们报告了同样在植物染色体中来源于正链、负链和双链 RNA 病毒的内源性 NRVS。这些序列是通过搜索公共基因组序列数据库发现的，重要的是，大多数 NRVS 随后通过对植物 DNA 的直接分子分析被检测到。最广泛的 NRVS 与双节段 dsRNA 基因组的二分体病毒科的外壳蛋白（CP）基因有关，其中包括感染植物和真菌的成员。一种新型真菌病毒（Rosellinia necatrix partitivirus 2，RnPV2）的 CP 与拟南芥 ILR2 的序列相似度最高，ILR2 被认为调节植物激素生长素吲哚-3-乙酸（IAA）的活性。此外，在广泛的植物物种中，鉴定出与植物二分体病毒比 RnPV2 更密切相关的二分体病毒 CP 样序列。此外，细胞弹状病毒和多瘤病毒的核衣壳蛋白基因在包括十字花科和茄科在内的 9 个以上植物科的物种中被发现。在黄瓜基因组中鉴定出一种 betaflexivirus 的复制酶样序列。NRVS 的出现模式以及 NRVS 和相关病毒的系统发育分析表明，可能发生了多次独立整合到许多植物谱系中。例如，一个 NRVS 保留在拟南芥中，但不在拟南芥或其他相关荠属物种中，而另一个 NRVS 则表现出相反的模式。我们的研究表明，单链和双链 RNA 病毒序列广泛存在于植物基因组中，并且展示了整合到基因组中的 NRVS 有潜力解决植物物种中不明确的系统发育关系。
