Leucoma salicis nucleopolyhedrovirus (LesaNPV) genome sequence shed new light on the origin of the Alphabaculovirus orpseudotsugatae species

Abstract

LesaNPV (Leucoma salicis nucleopolyhedrovirus) is an alphabaculovirus group Ib. Potentially, it can be an eco-friendly agent to control the white satin moth Leucoma salicis population. In this study, we have established the relationship between LesaNPV and other closely related alphabaculoviruses. Environmental samples of late instar of white satin moth collected in Poland infected with baculovirus have been homogenized, polyhedra were purified and subjected to scanning and transmission electron microscopy. Viral DNA was sequenced using the Illumina platform and the whole-genome sequence was established by de novo assembly of paired reads. Genome annotation and phylogenetic analyses were performed with the use of bioinformatics tools. The genome of LesaNPV is 132 549 bp long with 154 ORFs and 54.9% GC content. Whole-genome sequencing revealed deletion of dUTPase as well as ribonucleoside reductases small and large subunits region in LesaNPV genome compared to Dasychira pudibunda nucleopolyhedrovirus (DapuNPV) and Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV) where this region is complete. Phylogenetic analysis of Baculoviridae family members showed that LesaNPV is less divergent from a common ancestor than closely related species DapuNPV and OpMNPV. This is interesting because their hosts do not occur in the same area. The baculoviruses described in this manuscript are probably isolates of one species and could be assigned to recently denominated species Alphabaculovirus orpseudotsugatae, historically originating from OpMNPV. This finding could have significant implications for the classification and understanding of the phylogeographical spread of baculoviruses.

Keywords: Leucoma salicis; Alphabaculovirus; Common ancestor; DapuNPV; LesaNPV; OpMNPV.

Fig. 1

World distribution of insect hosts Leucoma salicis, Dasychira pudibunda, and Orgyia pseudotsugata of baculoviruses LesaNPV, DapuNPV, and OpMNPV with schematic representation of their food preferences (conifers or deciduous trees). L. salicis has been reported to have been introduced to North America in the 1920s (created in biorender.com)

Fig. 2

Scanning (SEM, left panel) and Transmission Electron Microscopy (TEM, right panel) photographs of LesaNPV. Multiple nucleocapsids are embedded in polyhedral occlusion bodies

Fig. 3

Circular map of LesaNPV genome. Arrows indicate the orientation of putative ORFs, marked in light blue. Core genes are marked in dark blue, hrs in orange, and non-hr region in green

Fig. 4

Phylogenetic cladogram illustrating the relationship within the Baculoviridae family. Maximum likelihood molecular analysis of 96 baculoviruses was performed based on concatenated sequences of 38 proteins encoded by core genes, utilizing IQ-TREE software with CuniNPV as the outgroup. The percentage of 1000 ultrafast bootstrap replicates supporting each clustered grouping of baculoviruses are indicated adjacent to the branches. The genera Alphabaculovirus, Betabaculovirus, Gammabaculovirus, and Deltabaculovirus are presented. A notable cluster includes LesaNPV (green), OpMNPV (red), and DapuNPV (blue), which demonstrate close evolutionary relationships

Fig. 5

Gene-parity plot analysis. Gene-parity plots among LesaNPV, DapuNPV, and OpMNPV—three closely related alphabaculoviruses—where polh gene is considered a first gene. OpMNPV was adjusted by reverse complement of the whole genome so that polh is in the forward orientation, but original numbering of the ORFs stays unchanged. When there is no homolog ORF in the compared genome the ORF was treated as “0,” so is presented on “x”- or “y”-axis. Green dots indicate percentage of similarity of nucleotide sequences of homolog ORFs

Fig. 6

Schematic representation of an alignment of six nucleotide sequences of the region trgf-fgf, where rrss-dUTPase deletion occurs in LesaNPV in contrary to DapuNPV (ML1 and T1 isolates) and OpMNPV. DijuNPV and HycuNPV do not possess this region. On the left—FastTree for the presented region alignment is shown

Fig. 7

Host range factor-1 (HRF-1) amino acid sequences alignment from seven baculovirus isolates—LesaNPV, OpMNPV, DapuNPV, LdMNPV, OlmeNPV, ObpuNPV, and HycuNPV (China). Black indicates 100% similarity, a highly acidic region crucial for the function of HRF-1 (Ikeda et al., 2005) is marked with red rectangle

Fig. 8

Maximum Likelihood molecular analysis of different amino acid sequences of HRF-1 available in GenBank database (isolates with 100% similar sequences were omitted in the phylogenetic tree). The percentage of 1000 bootstrap replicates is presented next to the branches