The complete genome sequence of an alphabaculovirus from Spodoptera exempta, an agricultural pest of major economic significance in Africa

Abstract

Spodoptera exempta nucleopolyhedrovirus (SpexNPV) is a viral pathogen of the African armyworm, Spodoptera exempta (Lepidoptera: Noctuidae), a significant agricultural pest of cereal crops in Africa. SpexNPV has been evaluated as a potential insecticide for control of this pest and has served as the subject of research on baculovirus pathology and transmission. Occlusion bodies (OBs) of SpexNPV isolate 244.1 were examined, and the nucleotide sequence of the genome was determined and characterized. SpexNPV-244.1 OBs consisted of irregular polyhedra with a size and appearance typical for alphabaculoviruses. Virions within the polyhedra contained 1–8 nucleocapsids per unit envelope. The SpexNPV-244.1 genome was comprised of a 129,528 bp circular sequence, in which 139 ORFs were annotated. Five homologous regions (hrs) consisting of a variable number of 28-bp imperfect palindromes were identified in the genome. The genome sequence contained the 38 core genes of family Baculoviridae, as well as three ORFs unique to the SpexNPV sequence and one ORF that was apparently acquired by horizontal gene transfer with a betabaculovirus ancestor. Phylogenetic inference with core gene amino acid sequence alignments placed SpexNPV-244.1 in a lineage containing alphabaculoviruses of Spodoptera frugiperda and Spodopotera exigua which in turn is part of a larger group of alphabaculoviruses from the subfamily Noctuinae in the lepidopteran family Noctuidae. Kimura-2-parameter pairwise nucleotide distances indicated that SpexNPV-244.1 represented a different and previously unlisted species in the genus Alphabaculovirus. Gene parity plots indicated that the gene order of SpexNPV-244.l was extensively collinear with that of Spodoptera exigua NPV (SeMNPV). These plots also revealed a group of 17 core genes whose order was conserved in other alpha- and betabaculoviruses.

The History of Baculovirology in Africa

“…More recently, Redman et al [ 104 ] cloned an isolate of SpexNPV in vivo, identifying at least 17 genetically distinct genotypes, which varied in size from approximately 115 to 153 Kbp. Subsequently, Escasa et al [ 105 ] reported fully sequencing the genome of a SpexNPV isolate, collected in Tanzania in the 1970s, and thus very likely the same isolate as investigated by Redman et al [ 104 ]. The genome was 129.5 Kbp.…”

Caracterización de baculovirus autóctonos para el control de la oruga militar tardía (<i>Spodoptera frugiperda</i>)

“…A partir del mapeo genómico de los genes correspondientes a estas proteínas estructurales, se observó una elevada sintenia en este grupo de genes de EpapGV y SfGV (Figuras 2.3 y 2.4). Más aún, en ambos granulovirus se confirmó la presencia de una región colineal densamente poblada con core genes estructurales (región colineal baculoviral), que ha sido descripta previamente en otras especies de baculovirus 133,134 y se postula como un elemento genómico conservado en los géneros Alphabaculovirus y Betabaculovirus. La comparación entre los proteomas de distintos miembros de la familia Baculoviridae evidenció que esta región, en comparación con el resto del genoma viral, se encuentra densamente ocupado por secuencias codificantes asociadas con funciones estructurales (Figuras 2.5).…”