Title of article :
Nucleotide-Resolution Profiling of RNA Recombination in the Encapsidated Genome of a Eukaryotic RNA Virus by Next-Generation Sequencing
Author/Authors :
Andrew Routh، نويسنده , , Phillip Ordoukhanian، نويسنده , , John E. Johnson، نويسنده ,
Issue Information :
روزنامه با شماره پیاپی سال 2012
Pages :
13
From page :
257
To page :
269
Abstract :
Next-generation sequencing has been used in numerous investigations to characterize and quantify the genetic diversity of a virus sample through the mapping of polymorphisms and measurement of mutation frequencies. Next-generation sequencing has also been employed to identify recombination events occurring within the genomes of higher organisms, for example, detecting alternative RNA splicing events and oncogenic chromosomal rearrangements. Here, we combine these two approaches to profile RNA recombination within the encapsidated genome of a eukaryotic RNA virus, flock house virus. We detect hundreds of thousands of recombination events, with single-nucleotide resolution, which result in diversity in the encapsidated genome rivaling that due to mismatch mutation. We detect previously identified defective RNAs as well as many other abundant and novel defective RNAs. Our approach is exceptionally sensitive and unbiased and requires no prior knowledge beyond the virus genome sequence. RNA recombination is a powerful driving force behind the evolution and adaptation of RNA viruses. The strategy implemented here is widely applicable and provides a highly detailed description of the complex mutational landscape of the transmissible viral genome.
Keywords :
virus-like particles , defective RNAs , deep sequencing , flock house virus
Journal title :
Journal of Molecular Biology
Serial Year :
2012
Journal title :
Journal of Molecular Biology
Record number :
1255000
Link To Document :
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