The comparative analysis of complete genome sequences from two South African betabaculoviruses: Phthorimaea operculella granulovirus and Plutella xylostella granulovirus

Abstract

The complete genomes of two novel South African betabaculovirus isolates, namely Phthorimaea operculella granulovirus (PhopGV-SA) and Plutella xylostella granulovirus (PlxyGV-SA), were sequenced and compared to the respective reference isolates PhopGV-1346 and PlxyGV-K1. For both isolates, the genome size and guanine-cytosine (GC) content were similar to those of the respective reference genomes. However, numerous-single nucleotide polymorphisms (SNPs) and several insertions/deletions were observed, revealing the novelty of the isolates. Focus was placed on analysing the observed insertion/deletion events by conducting amino acid sequence alignments for all ORFs of each isolate against all respective ORFs in the corresponding reference isolate. Certain ORFs in each granulovirus genome contained significant insertion/deletion events. In addition, the PlxyGV-SA genome had single-nucleotide insertions/deletions in ORFs 38 and 49 that resulted in the extension and complete overlap of these two ORFs with the neighbouring ORFs 39 and 48, respectively. These novel isolates have significant potential for development and application as biopesticides in South Africa, and the genetic variations observed may have important implications for the biological activity and management of host resistance in the field.

Effects of a Covert Infection with Phthorimaea operculella granulovirus in Insect Populations of Phthorimaea operculella

“…One method to obtain new baculoviruses is to collect insects from field populations and rear them in the laboratory until a virus outbreak occurs. This method has been successfully applied to isolate betabaculoviruses from various insects and environments, such as South-African strains of Phthorimaea operculella granulovirus (PhopGV-SA), Plutella xylostella granulovirus (PlxyGV-SA) and Cryptophlebia leucotreta granulovirus (CrleGV-SA) [16,17,18]. The latter was obtained after overcrowding larvae of a reared Thaumatotibia leucotreta colony.…”

“…Phthorimaea operculella granulovirus (PhopGV) (genus Betabaculovirus, family Baculoviridae ) is a dsDNA virus with a circular genome of about 119 kb, encoding 130 open reading frames (ORF), [16,31]. It can infect several members of the lepidopteran family Gelechiidae like Phthorimaea operculella , Tuta absoluta , Tecia solanivora and others [32,33,34].…”

Reads in a haystack: extracting complete mitogenome sequences hidden in baculovirus datasets

“…While representing around only 0.006% of the data analysed, three datasets contained enough reads to achieve suitable coverage across the entire sequence, with fewer mtDNA reads detected in at least 9 other sets. The application of this process to baculovirus datasets obtained from other insect pests, such as C. peltastica or P. operculella (Jukes et al, 2016;Marsberg et al, 2018), could enable the rapid generation of novel mitochondrial sequences and improve molecularbased techniques used to monitor pests in the field (see for example Timm et al, 2007;Meraner et al, 2008;Timm et al 2008;Li et al, 2015;Mgocheki and Addison, 2016). Comparison between each of the assembled sequences indicated a high degree of identity, with ambiguities affecting less than 0.3% of all nucleotides called.…”

“…For example, the baculovirus Cryptophlebia leucotreta granulovirus (CrleGV) has been the subject of significant research and development for use as a biological control agent against its homologous host, T. leucotreta. In recent years, complete genome sequences for several baculovirus species have been determined (Aragao-Silva et al, 2016;Jukes et al, 2016;Harrison et al, 2018;Marsberg et al, 2018;Trentin et al, 2019). When processing data generated by NGS platforms for baculovirus samples, most of the reads typically originate from the targeted virus, however, any non-target host, bacterial, viral, or other contaminating DNA present in samples will also be sequenced.…”

The potential of novel African isolates of Phthorimaea operculella granulovirus for the control of Tuta absoluta

“…It is a dsDNA virus with a genome of about 119 kbp encoding 130 open reading frames (ORFs). Full genome sequences of PhopGV isolates have been determined for the Tunisian isolate PhopGV-1346 and the South African isolate PhopGV-SA (Jukes, Motsoeneng, Knox, Hill, & Moore, 2016;Taha, Nour-El-Din, Croizier, López Ferber, & Croizier, 2000). Genetic variability of PhopGV isolates is demonstrated by endonuclease restriction digestion of the genomic DNA (Espinel-Correal et al, 2010;Lery, Abol-Ela, & Giannotti, 1998) as well as PCR analysis of specific genome areas (Carpio et al, 2013;Jukes, Knox, Hill, & Moore, 2014).…”