Nanopore reads spanning the whole genome of arthropod-infecting large dsDNA viruses of the class Naldaviricetes enable assembly-free sequence analysis

Abstract

The nuclear arthropod-specific large DNA viruses comprise different phylogenetically related virus families (Baculoviridae, Nudiviridae, Hytrosaviridae and Nimaviridae) forming the class Naldaviricetes. One common characteristic of their large double-stranded circularly and covalently closed DNA genomes is the size of up to hundreds of kilobase pairs, encoding up to hundreds of open reading frames. Until recently, analyzing such large viral dsDNA genomes was hampered by short read sequencing techniques, requiring bioinformatic assembly strategies to construct a consensus sequence as a descriptor of a population of haplotype sequences. The ideal aim for decoding large dsDNA genomes is an assembly-free method that allows the individual gnomes of a virus population to be sequenced in individual reads without fragmentation. Such full-length genome sequencing of single genome molecules is made possible by Nanopore sequencing, which is increasingly used to decode representatives of the Naldaviricetes. The present study discusses the impact of Nanopore sequencing on the characterization of viral NALDV populations. Full-length genome reads can be found in published sequence data from Bombyx mori nucleopolyhedrovirus (BmNPV; family Baculoviridae) and Oryctes rhinoceros nudivirus (OrNV; family Nudiviridae) isolates, providing insight into the future of deciphering populations of members of the order Lefavirales and class Naldaviricetes. Thirty years after the first sequencing of a baculovirus in 1994, a new era of sequencing of arthropod-infecting large dsDNA viruses has begun, which will allow assembly-free analysis of entire populations of large dsDNA viruses.