RESUMO
Twelve complete genome sequences of Phthorimaea operculella granulovirus (PhopGV) isolates from four different continents (Africa, South America, Asia and Europe) were analysed after Illumina next-generation sequencing (NGS). The isolates have a circular double-stranded DNA genome that is 118â355 to 119â177 bp in length and all of them encode 130 open reading frames (ORFs). Analysis of single-nucleotide polymorphisms (SNPs) revealed a unique set of SNP positions for every tested isolate. The genome sequences of the investigated PhopGV isolates were classified into a new system of four (1-4) groups according to the presence of group-specific SNPs as well as insertions and deletions. These genome groups correlated with phylogenetic lineages inferred from minimum-evolution trees of the whole-genome consensus nucleotide sequences. All members of group 3 originated from the Mediterranean area, whereas the geographical origin and the group assignment did not correlate for isolates belonging to genome groups 1, 2 or 4. The high degree of coverage facilitated the determination of variant nucleotide frequencies. We conclude that the geographical isolates of PhopGV are genetically highly similar. On the other hand, they were rarely genetically homogenous and in most cases appeared to be mixtures of multiple genotypes.
Assuntos
Granulovirus/genética , Lepidópteros/virologia , Mariposas/virologia , Polimorfismo de Nucleotídeo Único/genética , África , Animais , Ásia , DNA Viral/genética , Europa (Continente) , Genoma Viral/genética , Genótipo , Larva/virologia , Fases de Leitura Aberta/genética , Filogenia , Análise de Sequência de DNA/métodos , América do SulRESUMO
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.