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

Abstract

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.

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

“…BLASTx queries with PastNPV-473 ORFs yielded top matches predominantly with group I alphabaculoviruses, including Lonomia obliqua multiple nucleopolyhedrovirus (LoobMNPV [ 27 ], 29 ORFs), Bombyx mori nucleopolyhedrovirus (BmNPV [ 28 ]; 20 ORFs), Rachiplusia ou multiple nucleopolyhedrovirus (RoMNPV [ 29 ], 11 ORFs), Catopsilia pomona nucleopolyhedrovirus (CapoNPV [ 30 ], 11 ORFs), Thysanoplusia orichalcea nucleopolyhedrovirus (ThorNPV [ 31 ], 10 ORFs), Autographa californica multiple nucleopolyhedrovirus ([ 32 ], 8 ORFs), Maruca vitrata nucleopolyhedrovirus (MaviNPV [ 33 ], 6 ORFs), Plutella xylostella multiple nucleopolyhedrovirus (PlxyMNPV [ 34 ], 6 ORFs), and Troides aeacus nucleopolyhedrovirus (TraeNPV [ 35 ], 4 ORFs). Another 11 PastNPV ORFs exhibited matches with one or two ORFs each from eleven other alphabaculoviruses ( Table S2 ).…”

The complete mitochondrial genome of Attacus atlas formosanus Villiard, 1969 (Lepidoptera: Saturniidae)

“…Total genomic DNA was extracted from a mixture of nucleopolyhedrovirus (NPV) infected larvae and conducted to DNA sequencing by following the previously published methods (Huang et al. 2019 ). Reference-assisted de novo assembly approach was utilized by using MIRA assembler (Chevreux et al.…”