PMID- 31133070 OWN - NLM STAT- MEDLINE DCOM- 20190912 LR - 20200225 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 20 IP - 1 DP - 2019 May 27 TI - Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features. PG - 419 LID - 10.1186/s12864-019-5713-2 [doi] LID - 419 AB - 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. FAU - Huang, Yu-Feng AU - Huang YF AD - Genomics Research Center, Academia Sinica, Taipei, Taiwan. FAU - Chen, Tzu-Han AU - Chen TH AD - Genomics Research Center, Academia Sinica, Taipei, Taiwan. FAU - Chang, Zih-Ting AU - Chang ZT AD - Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan. FAU - Wang, Tai-Chuan AU - Wang TC AD - Department of Entomology, National Taiwan University, Taipei, Taiwan. FAU - Lee, Se Jin AU - Lee SJ AD - Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea. FAU - Kim, Jong Cheol AU - Kim JC AD - Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea. FAU - Kim, Jae Su AU - Kim JS AD - Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea. FAU - Chiu, Kuo-Ping AU - Chiu KP AD - Genomics Research Center, Academia Sinica, Taipei, Taiwan. FAU - Nai, Yu-Shin AU - Nai YS AD - Department of Entomology, National Chung Hsing University, Taichung, Taiwan. ysnai@nchu.edu.tw. LA - eng PT - Journal Article DEP - 20190527 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (DNA, Viral) RN - 0 (Viral Structural Proteins) SB - IM MH - Animals MH - Baculoviridae/classification/*genetics/isolation & purification MH - Butterflies/growth & development/*virology MH - DNA Replication MH - DNA, Viral/chemistry MH - Genes, Duplicate MH - Genes, Viral MH - *Genome, Viral MH - Genomics MH - Host Specificity/genetics MH - Larva/virology MH - Open Reading Frames MH - Phylogeny MH - Sequence Homology, Nucleic Acid MH - Transcription, Genetic MH - Viral Structural Proteins/genetics PMC - PMC6537400 OTO - NOTNLM OT - TraeNPV OT - Troides aeacus OT - Troides aeacus nucleopolyhedrovirus COIS- The authors declare that they have no competing interests. EDAT- 2019/05/28 06:00 MHDA- 2019/09/13 06:00 PMCR- 2019/05/27 CRDT- 2019/05/29 06:00 PHST- 2018/07/31 00:00 [received] PHST- 2019/04/17 00:00 [accepted] PHST- 2019/05/29 06:00 [entrez] PHST- 2019/05/28 06:00 [pubmed] PHST- 2019/09/13 06:00 [medline] PHST- 2019/05/27 00:00 [pmc-release] AID - 10.1186/s12864-019-5713-2 [pii] AID - 5713 [pii] AID - 10.1186/s12864-019-5713-2 [doi] PST - epublish SO - BMC Genomics. 2019 May 27;20(1):419. doi: 10.1186/s12864-019-5713-2.