Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus.

Jörg T Wennmann,Karolin E Eberle,Pit Radtke,Johannes A Jehle,Gianpiero Gueli Alletti

doi:10.3390/v9080227

Jörg T Wennmann, Karolin E Eberle + Show 3 more

Open Access

https://doi.org/10.3390/v9080227

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Abstract

Six complete genome sequences of Cydia pomonella granulovirus (CpGV) isolates from Mexico (CpGV-M and CpGV-M1), England (CpGV-E2), Iran (CpGV-I07 and CpGV-I12), and Canada (CpGV-S) were aligned and analyzed for genetic diversity and evolutionary processes. The selected CpGV isolates represented recently identified phylogenetic lineages of CpGV, namely, the genome groups A to E. The genomes ranged from 120,816 bp to 124,269 bp. Several common differences between CpGV-M, -E2, -I07, -I12 and -S to CpGV-M1, the first sequenced and published CpGV isolate, were highlighted. Phylogenetic analysis based on the aligned genome sequences grouped CpGV-M and CpGV-I12 as the most derived lineages, followed by CpGV-E2, CpGV-S and CpGV-I07, which represent the most basal lineages. All of the genomes shared a high degree of co-linearity, with a common setup of 137 (CpGV-I07) to 142 (CpGV-M and -I12) open reading frames with no translocations. An overall trend of increasing genome size and a decrease in GC content was observed, from the most basal lineage (CpGV-I07) to the most derived (CpGV-I12). A total number of 788 positions of single nucleotide polymorphisms (SNPs) were determined and used to create a genome-wide SNP map of CpGV. Of the total amount of SNPs, 534 positions were specific for exactly one of either isolate CpGV-M, -E2, -I07, -I12 or -S, which allowed the SNP-based detection and identification of all known CpGV isolates.

Highlights

The Cydia pomonella granulovirus (CpGV) is a double-stranded DNA virus that constitutes the type species Cydia pomonella granulovirus of the genus Betabaculovirus [1,2]
The coverage was considered sufficient as major differences between CpGV-I12 and the reference genome CpGV-M1 [5] were already known by restriction length polymorphism (RFLP) analysis and partial sequencing [7]
CpGV-M1 was removed from the whole genome alignment, and the genome sequence of Cryptophlebia leucotreta granulovirus (CrleGV) (NC_005068) was included in the alignment

Summary

Introduction

The Cydia pomonella granulovirus (CpGV) is a double-stranded DNA (dsDNA) virus that constitutes the type species Cydia pomonella granulovirus of the genus Betabaculovirus (family Baculoviridae) [1,2]. The category of a virus species is defined as “a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche” [19,20] It is an assemblage of narrowly related isolates, which may differ in single characteristics such as nucleotide sequence, protein composition, virulence etc., yet share enough similarities to comply with this definition. After the genome sequencing of different CpGV isolates was performed to identify the major target of type I resistance [5], we had the unique opportunity to use the whole genome sequences for studying the diversity, phylogeny, and evolutionary trends within a baculovirus species. We focused on the detection of SNPs of the five entirely sequenced isolates to create a genome-wide map of genome group, and multiple genome group-specific SNP positions

CpGV Isolates and Sequences

Genome Sequencing

Genome Analysis

Phylogenetic Analysis

Results and Discussion

Graphical alignment of to