Abstract
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.
Highlights
The genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and interactions between viruses and their hosts
Most of the partitivirus-like sequences (18) were discovered from plant cDNA libraries, including those of 10 monocots, 19 eudicots, and 3 conifers, but only two were found in fungal cDNA libraries, these viruses are common in different fungal species
The capsid protein (CP)-like sequences from cDNA libraries of flatworm (Schistosoma mansoni) and twisted-wing parasite (Mengenilla chobauti) were most closely related to those of certain fungal viruses in clade I and III (Fig. 3). If these sequences were derived from viruses infecting the annotated hosts, these results clearly suggest that horizontal transmission of these viruses occurred between animals and fungi or between animals and plants
Summary
The genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and interactions between viruses and their hosts. Recent viral metagenomic studies overcame these limitations and provided a promising method for investigation of unrefined viral diversity, in which viral particles are first partially purified and viral sequences are randomly amplified before sub-cloning and sequencing [3,4] By using this approach, numerous previously unknown viruses have been discovered in environmental and clinical samples [5,6,7,8]. With the advance of generation sequencing (NGS) technologies, another culture-independent approach for virus discovery is developed by deep sequencing and assembly of virus-derived small silencing RNAs [9,10,11] This approach can identify both plant and invertebrate viruses occurring at extremely low titers without purification of viral particles and amplification of viral sequences
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
