Abstract
Natural isolates of baculoviruses (as well as other dsDNA viruses) generally consist of homogenous or heterogenous populations of genotypes. The number and positions of single nucleotide polymorphisms (SNPs) from sequencing data are often used as suitable markers to study their genotypic composition. Identifying and assigning the specificities and frequencies of SNPs from high-throughput genome sequencing data can be very challenging, especially when comparing between several sequenced isolates or samples. In this study, the new tool “bacsnp”, written in R programming langue, was developed as a downstream process, enabling the detection of SNP specificities across several virus isolates. The basis of this analysis is the use of a common, closely related reference to which the sequencing reads of an isolate are mapped. Thereby, the specificities of SNPs are linked and their frequencies can be used to analyze the genetic composition across the sequenced isolate. Here, the downstream process and analysis of detected SNP positions is demonstrated on the example of three baculovirus isolates showing the fast and reliable detection of a mixed sequenced sample.
Highlights
In recent years, sequencing of genomes of large dsDNA viruses has been facilitated by the availability of whole genome sequencing techniques that allow deciphering of genomes in relatively short time with up to thousands-fold read depth [1]
On the example of three isolates of the Cydia pomonella granulovirus species (CpGV) [2], we describe how a consensus sequence free method can be used to detect isolate or specimen-specific SNPs positions and how those can be used to decipher the genotypic composition of isolates
Based on the paired reads alone, an entire coverage of the reference genome was given with read depths up to 3000 for CpGV-M and -S, which was ensured by the large proportion of reads that mapped to CpGV-M and CpGV-E2, respectively (Table 1)
Summary
In recent years, sequencing of genomes of large dsDNA viruses has been facilitated by the availability of whole genome sequencing techniques that allow deciphering of genomes in relatively short time with up to thousands-fold read depth [1]. One of the largest groups of dsDNA viruses are baculoviruses (family Baculoviridae, [2]), which are specific for insects from the orders Lepidoptera, Hymenoptera and Diptera. Their genomes are 80 to 180 kbp long and encode 100 to 200 open reading frames long [2]. Since numerous baculoviruses are used as biological pest control agents, there is a considerable scientific and economic interest in the identification of isolates and the elucidation of genetic variability
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