The Parapoynx stagnalis Nucleopolyhedrovirus (PastNPV), a Divergent Member of the Alphabaculovirus Group I Clade, Encodes a Homolog of Ran GTPase

Abstract

We report the analysis of the genome of a novel Alphabaculovirus, Parapoynx stagnalis nucleopolyhedrovirus isolate 473 (PastNPV-473), from cadavers of the rice case bearer, Parapoynx stagnalis Zeller (Lepidoptera: Crambidae), collected in rice fields in Kerala, India. High-throughput sequencing of DNA from PastNPV occlusion bodies and assembly of the data yielded a circular genome-length contig of 114,833 bp with 126 annotated opening reading frames (ORFs) and six homologous regions (hrs). Phylogenetic inference based on baculovirus core gene amino acid sequence alignments indicated that PastNPV is a member of the group I clade of viruses in genus Alphabaculovirus, but different phylogenetic methods yielded different results with respect to the placement of PastNPV and four similarly divergent alphabaculoviruses in the group I clade. Branch lengths and Kimura-2-parameter pairwise nucleotide distances indicated that PastNPV-473 cannot be classified in any of the currently listed species in genus Alphabaculovirus. A unique feature of the PastNPV genome was the presence of an ORF encoding a homolog of Ran GTPase, a regulator of nucleocytoplasmic trafficking. PastNPV appears to have acquired a homolog of Ran relatively recently from a lepidopteran host via horizontal gene transfer.

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants

“…The disadvantage of this method is the short length of the reads, which is usually between 50 and 300 nt (mostly 150 nt). To reconstruct a representative baculovirus sequence, a so-called consensus, from up to millions of reads, a de novo or reference-based assembly is usually applied [18][19][20]. The generation of consensus sequences risks masking intra-isolate genetic variability, as baculovirus isolates are usually composed of different haplotypes, single DNA molecules (=baculovirus genome) with all their DNA variations, due to differential replication, mutation and selection within the host [21][22][23][24].…”