Comparative genomics of the Neodiprion sertifer nucleopolyhedrovirus from Turkey with the fewest ORFs among baculoviruses

Abstract

Abstract The complete genome of the European pine sawfly Neodiprion sertifer nucleopolyhedrovirus was sequenced and characterized from next-generation sequencing data of the N. sertifer larva from Turkiye. This genome was comparatively analysed by previously reported genomes baculoviruses. The baculovirus phylogeny was reconstructed and the species boundary of the NeseNPV-TR was delineated using K2P distance. The length of the genome was 82,052 bp, with a G + C content of 33.28%. It contained 82 putative ORFs, including 33 baculovirus core genes, three lepidopteran baculovirus core genes, three non-conserved genes. It had five hrs with 20.6% overall mean distance on average. The pairwise K2P distances of lef-9 and polh genes were lower than the specified threshold value, while those of lef-8, combinations of three genes and 33 genes were slightly higher between NeseNPV-TR and NeseNPV. The most variable genes were lef-2, helicase, p40, desmoplakin, p6.9, vp91 and vp39, while the most conserved were lef-8, lef-9, odv-e18, pif2 and lef-5 among baculoviruses. The genome of NeseNPV-TR is smaller and contains the fewest ORFs among baculoviruses. Some of unassigned ORFs had conserved domains and hence, we suggest further investigation to determine their structural and functional roles. Phylogenetic analyses confirmed its position within Gammabaculovirus. The NeseNPV-TR can be considered as the same species with NeseNPV. The different divergence rates in the baculovirus core genes may be related with different selection pressures acting on the genes. The lower genetic diversity of Group I alphabaculoviruses is most probably due to recent emergence.