Protein-Gene Orthology in Baculoviridae: An Exhaustive Analysis to Redefine the Ancestrally Common Coding Sequences

Abstract

Baculoviruses are entomopathogens that carry large, double-stranded circular DNA genomes and infect insect larvae of Lepidoptera, Hymenoptera and Diptera, with applications in the biological control of agricultural pests, in the production of recombinant proteins and as viral vectors for various purposes in mammals. These viruses have a variable genetic composition that differs between species, with some sequences shared by all known members, and others that are lineage-specific or unique to isolates. Based on the analysis of nearly 300 sequenced genomes, a thorough bioinformatic investigation was conducted on all the baculoviral protein coding sequences, characterizing their orthology and phylogeny. This analysis confirmed the 38 protein coding sequences currently considered as core genes, while also identifying novel coding sequences as candidates to join this set. Accordingly, homology was found among all the major occlusion body proteins, thus proposing that the polyhedrin, granulin and CUN085 genes be considered as the 39th core gene of Baculoviridae.

Genome assembly and annotation of Spilosoma obliqua multicapsid nucleopolyhedrovirus from Bihar hairy caterpillar, an agriculturally important insect pest

“…The SpobMNPV has all the 38 core genes (Cerrudo et al, 2023) (Table S3) reported in baculoviruses and is highly similar to their TA B L E 1 Whole-genome comparison of SpobMNPV isolate with some selected baculoviruses. 138) 62 ( 15) 78 ( 136) 79 ( 14) 79 ( 14)…”

“…Although p24 is identified as a conserved gene among lepidopteran baculoviruses (Rohrmann, 2019), further analysis of the function of p24 is required in various baculoviruses to clarify its conserved role in OB shape among baculovirus species (Kokusho & Katsuma, 2021). However, before a recent report (Cerrudo et al, 2023), the presence of 38 core genes in baculoviruses has been considered widely for evolutionary studies.…”

A Comprehensive Study of MicroRNA in Baculoviruses

“…A recent study, which considered all available baculoviral genome data, proposed a similar outcome solely based on genetic distance criteria. This study explored sequences ranging between 81,755 and 178,733 base pairs and encompassed between 89 and 183 protein-coding genes [ 12 ]. Baculoviruses possess their own machinery for transcription and replication, and all reported members share at least 39 orthologous protein genes [ 12 , 13 , 14 ].…”

“…This study explored sequences ranging between 81,755 and 178,733 base pairs and encompassed between 89 and 183 protein-coding genes [ 12 ]. Baculoviruses possess their own machinery for transcription and replication, and all reported members share at least 39 orthologous protein genes [ 12 , 13 , 14 ]. Interestingly, despite the extensive protein gene content in baculoviral genomes, the presence of non-coding RNA genes has also been observed, including those that encode microRNAs (miRNAs) [ 15 ] and even transfer RNAs (tRNAs) [ 16 ].…”

“…The reported bac-miRs overlap with protein-coding regions, some of which have orthologs (core genes) in all known baculoviral genomes [ 12 ], including bmnpv-miR-3, AcMNPV-miR-1, AcMNPV-miR-3, AcMNPV-miR-5, agmnpv-miR-4, and Splt-NPV-miR-11698-3p. The remaining bac-miRs (except for bmnpv-miR 4) are not only located within alphabaculovirus coding genes but also within those of other genera.…”