Comparative Genome Sequence Analysis of Choristoneura occidentalis Freeman and C. rosaceana Harris (Lepidoptera: Tortricidae) Alphabaculoviruses

Abstract

The complete genome sequences of Choristoneura occidentalis and C. rosaceana nucleopolyhedroviruses (ChocNPV and ChroNPV, respectively) (Baculoviridae: Alphabaculovirus) were determined and compared with each other and with those of other baculoviruses, including the genome of the closely related C. fumiferana NPV (CfMNPV). The ChocNPV genome was 128,446 bp in length (1147 bp smaller than that of CfMNPV), had a G+C content of 50.1%, and contained 148 open reading frames (ORFs). In comparison, the ChroNPV genome was 129,052 bp in length, had a G+C content of 48.6% and contained 149 ORFs. ChocNPV and ChroNPV shared 144 ORFs in common, and had a 77% sequence identity with each other and 96.5% and 77.8% sequence identity, respectively, with CfMNPV. Five homologous regions (hrs), with sequence similarities to those of CfMNPV, were identified in ChocNPV, whereas the ChroNPV genome contained three hrs featuring up to 14 repeats. Both genomes encoded three inhibitors of apoptosis (IAP-1, IAP-2, and IAP-3), as reported for CfMNPV, and the ChocNPV IAP-3 gene represented the most divergent functional region of this genome relative to CfMNPV. Two ORFs were unique to ChocNPV, and four were unique to ChroNPV. ChroNPV ORF chronpv38 is a eukaryotic initiation factor 5 (eIF-5) homolog that has also been identified in the C. occidentalis granulovirus (ChocGV) and is believed to be the product of horizontal gene transfer from the host. Based on levels of sequence identity and phylogenetic analysis, both ChocNPV and ChroNPV fall within group I alphabaculoviruses, where ChocNPV appears to be more closely related to CfMNPV than does ChroNPV. Our analyses suggest that it may be appropriate to consider ChocNPV and CfMNPV as variants of the same virus species.

The complete genome of a baculovirus isolated from an insect of medical interest: Lonomia obliqua (Lepidoptera: Saturniidae)

“…4b ), we have observed that unique ORFs in LoobMNPV (gaps with no correspondence to the other genomes) are interestingly found near hrs . According to previous reports, gene rearrangements and acquisitions are of common occurrence on proximities of hrs 20 , confirming the possibility of gene transfers to viruses by homologous recombination 21 , which could be also facilitated by factors such as the prevalence of various pathogens infecting the same host 22 , as well as concomitant infections in field populations 23 .…”

Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features

“…TraeNPV contains 35 baculovirus structural genes, which were listed by Hayakawa et al (2000), Jehle et al (2006) and Thumbi et al (2013) [5, 21, 24], and only the p15 (Ac87) gene was absent from the TraeNPV genome (Table 2). Of the 35 structural proteins, the P74 protein is associated with occluded virions and is required for oral infectivity [25, 26]; the VP1054 protein is required for AcMNPV nucleocapsid formation [27]; the P10 protein has been shown to be involved in the formation and stability of polyhedra and may influence cell lysis late in infection [28–30]; VP80 is associated with both ODV and BV in AcMNPV and OpMNPV [31, 32]; and ORF1629 is associated with the basal end of nucleocapsids and is essential for AcMNPV viability [33, 34].…”

“…A total of 13 genes involved in late baculovirus gene transcription that are all present on other baculovirus genomes [5, 21, 24] are also present in the TraeNPV genome, including lef 4–12 , 39 K , p47, vlf-1 and pe38 (Table 2). Of these genes, 10 genes ( lef-4~ − 6, − 8~ − 12, 39 k, and p47 ) are required for optimal levels of late gene transcription in the AcMNPV genome [40, 41].…”

“…A major group of conserved genes involved in DNA replication was described previously [5, 21, 24, 47]. AcMNPV and OpMNPV contain 5 genes that are essential for transient DNA replication ( ie-1, lef-1 , lef-2, lef-3 and helicase ) and 5 non-essential ones that stimulate transient DNA replication genes ( dna-pol, p35, ie-2, lef-7, and pe38 ) [48–50].…”

The genome sequence of Pseudoplusia includens single nucleopolyhedrovirus and an analysis of p26 gene evolution in the baculoviruses

“…The gene diversity in baculoviruses has been estimated to be about 900 genes, among which 37 (core genes) may play essential biological functions in the replication cycle [ 12 ]. The common genomic features of the Baculovirida e family include large double-stranded circular DNA, bidirectionally oriented open reading frames (ORFs) which are distributed on both DNA strands, 37 genes common to all baculoviruses (core genes), promoters that regulate the temporal cascade of gene expression and viral genome replication in the host cell nucleus [ 13 ].…”