Genome sequencing and organization of three geographically different isolates of nucleopolyhedrovirus from the gypsy moth reveal dignificant genomic differences
Erişim
info:eu-repo/semantics/closedAccessTarih
2023Yazar
Gencer, Dönüşİnan, Cihan
Bayramoğlu, Zeynep
Nalcacıoğlu, Remziye
Yin, Feifei
Zhu, Zheng
Wang, Jun
Hu, Zhihong
Pavlik, Lillian
Arif, Basil
Demirbağ, Zihni
Demir, İsmail
Üst veri
Tüm öğe kaydını gösterKünye
Gencer, D., Inan, C., Bayramoglu, Z., Nalcacioglu, R., Yin, F., Zhu, Z., Wang, J., Hu, Z., Pavlik, L., Arif, B., Demirbag, Z., & Demir, I. (2023). Genome Sequencing and Organization of Three Geographically Different Isolates of Nucleopolyhedrovirus from the Gypsy Moth Reveal Significant Genomic Differences. Current genomics, 24(3), 146–154. https://doi.org/10.2174/0113892029249830231014163829Özet
Background: The gypsy moth (Lymantria dispar L., Lepidoptera: Erebidae) is a worldwide pest of trees and forests. Lymantria dispar nucleopolyhedrovirus (LdMNPV) belongs to the Baculoviridae family and is an insect virus specific to gypsy moth larvae. In this study, we describe the complete genome sequences of three geographically diverse isolates, H2 (China), J2 (Japan), and T3 (Turkey), of Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV). Methods: The genomes of isolates H2, J2, and T3 were subjected to shotgun pyrosequencing using Roche 454 FLX and assembled using Roche GS De Novo Assembler. Comparative analysis of all isolates was performed using bioinformatics methods. Results: The genomes of LdMNPV-H2, J2, and T3 were 164,746, 162,249, and 162,614 bp in size, had GC content of 57.25%, 57.30%, and 57.46%, and contained 162, 165, and 164 putative open reading frames (ORFs ≥ 150 nt), respectively. Comparison between the reference genome LdMNPV-5/6 (AF081810) and the genomes of LdMNPV-H2, J2, and T3 revealed differences in gene content. Compared with LdMNPV-5/6, ORF5, 6, 8, 10, 31, and 67 were absent in LdMNPVH2, ORF5, 13, and 66 were absent in LdMNPV-J2, and ORF10, 13, 31, and 67 were absent in LdMNPV-T3. In addition, the gene encoding the mucin-like protein (ORF4) was split into two parts in isolates H2 and T3 and designated ORF4a and ORF4b. Phylogenetic analysis grouped isolates H2 and J2 in a different cluster than isolate T3, which is more closely related to the Turkish and Polish isolates. In addition, H2 was found to be closely related to a South Korean LdMNPV isolate. Conclusion: This study provided a more detailed overview of the relationships between different geographic LdMNPV isolates. The results showed remarkable differences between groups at the genome level.