State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China.
PLoS One. 2012;7(7):e42147. doi: 10.1371/journal.pone.0042147. Epub 2012 Jul 27.
Genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and the interaction between viruses and hosts. Traditional molecular cloning methods for obtaining RNA viral genomes are time-consuming and often difficult because many viruses occur in extremely low titers. DsRNA viruses in the families, Partitiviridae, Totiviridae, Endornaviridae, Chrysoviridae, and other related unclassified dsRNA viruses are generally associated with symptomless or persistent infections of their hosts. These characteristics indicate that samples or materials derived from eukaryotic organisms used to construct cDNA libraries and EST sequencing might carry these viruses, which were not easily detected by the researchers. Therefore, the EST databases may include numerous unknown viral sequences. In this study, we performed in silico cloning, a procedure for obtaining full or partial cDNA sequence of a gene by bioinformatics analysis, using known dsRNA viral sequences as queries to search against NCBI Expressed Sequence Tag (EST) database. From this analysis, we obtained 119 novel virus-like sequences related to members of the families, Endornaviridae, Chrysoviridae, Partitiviridae, and Totiviridae. Many of them were identified in cDNA libraries of eukaryotic lineages, which were not known to be hosts for these viruses. Furthermore, comprehensive phylogenetic analysis of these newly discovered virus-like sequences with known dsRNA viruses revealed that these dsRNA viruses may have co-evolved with respective host supergroups over a long evolutionary time while potential horizontal transmissions of viruses between different host supergroups also is possible. We also found that some of the plant partitiviruses may have originated from fungal viruses by horizontal transmissions. These findings extend our knowledge of the diversity and possible host range of dsRNA viruses and offer insight into the origin and evolution of relevant viruses with their hosts.
病毒的基因组序列对病毒进化、多样性以及病毒与宿主之间的相互作用的研究有很大的贡献。传统的获得 RNA 病毒基因组的分子克隆方法耗时且往往困难，因为许多病毒的滴度极低。在 Partitiviridae、Totiviridae、Endornaviridae、Chrysoviridae 等家族以及其他相关未分类的 dsRNA 病毒中，dsRNA 病毒通常与宿主无症状或持续性感染有关。这些特征表明，用于构建 cDNA 文库和 EST 测序的真核生物样品或材料可能携带这些病毒，而这些病毒很容易被研究人员忽略。因此，EST 数据库可能包含大量未知的病毒序列。在本研究中，我们使用已知的 dsRNA 病毒序列作为查询，通过生物信息学分析进行了计算机克隆，这是一种通过生物信息学分析获得基因的全长或部分 cDNA 序列的方法。通过这种分析，我们获得了 119 种与 Endornaviridae、Chrysoviridae、Partitiviridae 和 Totiviridae 家族成员相关的新型病毒样序列。其中许多在真核生物谱系的 cDNA 文库中被鉴定出来，但这些病毒的宿主并不为人所知。此外，对这些新发现的病毒样序列与已知 dsRNA 病毒的综合系统发育分析表明，这些 dsRNA 病毒可能在长期的进化过程中与各自的宿主超群共同进化，而不同宿主超群之间的病毒水平传播也是可能的。我们还发现，一些植物 Partitiviridae 可能是通过水平传播从真菌病毒中起源的。这些发现扩展了我们对 dsRNA 病毒多样性和可能宿主范围的认识，并为相关病毒及其宿主的起源和进化提供了新的视角。
