Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes.
Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes.
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DOI：
10.1371/journal.ppat.1002146
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发表时间：
2011-07
期刊：
影响因子：
6.7
通讯作者：
Suzuki N
中科院分区：
文献类型：
--
作者：
Chiba S;Kondo H;Tani A;Saisho D;Sakamoto W;Kanematsu S;Suzuki N
非逆转录病毒RNA病毒序列（NRVS）已在脊椎动物和真菌的染色体中发现，但不是植物。在这里，我们报告类似的内源性NRVS来自植物染色体中的正，负和双链RNA病毒。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随后通过植物DNA的直接分子分析检测到。最广泛的NRVS与具有双片段dsRNA基因组的部分病毒科的外壳蛋白（CP）基因相关，并且包括植物和真菌感染成员。一种新的真菌病毒（Rosellinia necatrix partitivirus 2，RnPV 2）的CP与拟南芥ILR 2具有最大的序列相似性，后者被认为调节植物激素生长素吲哚乙酸（IAA）的活性。此外，partitivirus CP-样序列更密切相关的植物partitiviruses比RnPV 2在广泛的植物物种中被确定。此外，在包括茄科、兰科等9个科的植物中发现了细胞弹状病毒和水痘病毒的核衣壳蛋白基因。在黄瓜基因组中鉴定出β-柔膜病毒的复制酶样序列。NRVS的发生模式和NRVS和相关病毒的系统发育分析表明，可能发生了多个独立的整合到许多植物谱系。例如，NRVS之一保留在Ar中。thaliana，而Ar. lyrata或其他相关的亚麻荠属物种，而另一个NRVS显示相反的模式。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，并显示了基因组整合NRVS有助于解决植物物种的系统发育关系不明确的潜力。真核生物基因组含有源自DNA病毒和逆转录病毒的序列，即，逆转录病毒、副逆转录病毒（DNA病毒）和转座子。然而，不能将其基因组转化为DNA的非逆转录病毒RNA病毒的序列直到最近才被认为不能整合到真核细胞核基因组中。我们提出的证据多个独立事件的水平基因转移从广泛的RNA病毒，包括正义，负义，和双链RNA病毒，到基因组的远亲植物谱系。一些非逆转录病毒整合的RNA病毒序列在植物科的属间是保守的，而另一些仅保留在属中有限数量的物种中。非逆转录病毒的整合RNA病毒序列的整合概况表明，这些序列作为强大的分子工具，破译相关植物之间的系统发育关系的潜力。此外，这项研究突出了植物选择非逆转录RNA病毒序列，并提供了深入了解植物基因组进化和非逆转录RNA病毒与其宿主之间的相互作用。
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. Eukaryotic genomes contain sequences that have originated from DNA viruses and reverse-transcribing viruses, i.e., retroviruses, pararetroviruses (DNA viruses), and transposons. However, the sequences of non-retroviral RNA viruses, which are unable to convert their genomes to DNA, were until recently considered not to be integrated into eukaryotic nuclear genomes. We present evidence for multiple independent events of horizontal gene transfer from a wide range of RNA viruses, including plus-sense, minus-sense, and double-stranded RNA viruses, into the genomes of distantly related plant lineages. Some non-retroviral integrated RNA viral sequences are conserved across genera within a plant family, whereas others are retained only in a limited number of species in a genus. Integration profiles of non-retroviral integrated RNA viral sequences demonstrate the potential of these sequences to serve as powerful molecular tools for deciphering phylogenetic relationships among related plants. Moreover, this study highlights plants co-opting non-retroviral RNA virus sequences, and provides insights into plant genome evolution and interplay between non-reverse-transcribing RNA viruses and their hosts.
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影响因子：
5.4
作者：
Gayral, Philippe;Noa-Carrazana, Juan-Carlos;Iskra-Caruana, Marie-Line
通讯作者：
Iskra-Caruana, Marie-Line
影响因子：
5.6
作者：
AGRANOVSKY, AA;BOYKO, VP;DOLJA, VV
通讯作者：
DOLJA, VV
影响因子：
2.7
作者：
Boccardo, G;Candresse, T
通讯作者：
Candresse, T
影响因子：
6.5
作者：
Anisimova, Maria;Gascuel, Olivier
通讯作者：
Gascuel, Olivier
DOI：
10.1073/pnas.0909766107
发表时间：
2010-10-26
影响因子：
11.1
作者：
Beilstein, Mark A.;Nagalingum, Nathalie S.;Mathews, Sarah
通讯作者：
Mathews, Sarah