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Background  The golden birdwing butterfly ( Troides aeacus formosanus ) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared  T. aeacus  larvae. From the previous Kimura-2 parameter (K-2-P) analysis based on the nucleotide sequence of three genes in this isolate,  polh ,  lef - 8  and  lef - 9 , the underlying virus did not belong to any known nucleopolyhedrovirus (NPV) species. Therefore, this NPV was provisionally named “TraeNPV”. To understand this NPV, the nucleotide sequence of the whole TraeNPV genome was determined using next-generation sequencing (NGS) technology.    Results  The genome of TraeNPV is 125,477 bp in length with 144 putative open reading frames (ORFs) and its GC content is 40.45%. A phylogenetic analysis based on the 37 baculoviral core genes suggested that TraeNPV is a Group I NPV that is closely related to  Autographa californica  nucleopolyhedrovirus (AcMNPV). A genome-wide analysis showed that TraeNPV has some different features in its genome compared with other NPVs. Two novel ORFs ( Ta75  and  Ta139 ), three truncated ORFs ( pcna ,  he65  and  bro ) and one duplicated ORF ( 38.7 K ) were found in the TraeNPV genome; moreover, there are fewer homologous regions (hrs) than there are in AcMNPV, which shares eight hrs within the TraeNPV genome. TraeNPV shares similar genomic features with AcMNPV, including the gene content, gene arrangement and gene/genome identity, but TraeNPV lacks 15 homologous ORFs from AcMNPV in its genome, such as  ctx ,  host cell-specific factor 1  ( hcf-1 ),  PNK/PNL ,  vp15,  and  apsup , which are involved in the auxiliary functions of alphabaculoviruses.    Conclusions  Based on these data, TraeNPV would be clarified as a new NPV species with defective AcMNPV genomic features. The precise relationship between TraeNPV and other closely related NPV species were further investigated. This report could provide comprehensive information on TraeNPV for evolutionary insights into butterfly-infected NPV.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5713-2) contains supplementary material, which is available to authorized users.

bmc genomics

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