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Comparative genomics of the Neodiprion sertifer nucleopolyhedrovirus from Turkey with the fewest ORFs among baculoviruses

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Abstract

The complete genome of a European pine sawfly Neodiprion sertifer nucleopolyhedrovirus (NeseNPV-TR) was sequenced and characterized from next-generation sequencing data of N. sertifer larva from Türkiye. This genome was analyzed and compared to previously reported genomes of baculoviruses. The baculovirus phylogeny was reconstructed and the species identity of the NeseNPV-TR was delineated using K2P distance. The length of the genome was 82,052 bp, with a G + C content of 33.28%. It contained 83 putative ORFs, including 38 baculovirus core genes, three lepidopteran baculovirus core genes, and three non-conserved genes. It had five hrs with 20.6% overall mean distance on average. The pairwise K2P distances of lef-8, lef-9, and polh genes and combinations of three genes and 38 genes between NeseNPV-TR and NeseNPV were slightly higher than the specified threshold values for species demarcation. The most variable genes were lef-2, helicase, p40, desmoplakin, pif7, p6.9, vp91, and vp39, while the most conserved were lef-8, lef-9, odv-e18, pif2, and lef-5 among baculoviruses. The genome of NeseNPV-TR is smaller and contains the fewest ORFs among baculoviruses. Some of unassigned ORFs had conserved domains and hence, we suggest further investigation to determine their structural and functional roles. Phylogenetic analyses confirmed its position within genus Gammabaculovirus. Taking into account the phylogenetic position, K2P distances, and NJ tree, the NeseNPV-TR can be classified in the same species (Gammabaculovirus nesertiferis) with NeseNPV. The different divergence rates in the baculovirus core genes may be related with different selection pressures acting on the genes. The lower genetic diversity of Group I alphabaculoviruses is most probably due to recent emergence.

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Data availability

The genome sequence generated in this study was deposited in the GenBank database under the Accession Number OP426321.

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Acknowledgements

We thank our colleagues from the Department of Biology of the Ege University who provided the specimens. We are also grateful to Dr. Hasan H. BAŞIBÜYÜK (Department of Gerontology, Akdeniz University) and Dr. Merve Nur AYDEMİR for their contributions in data generation. We thank the anonymous reviewers for their careful reading of the manuscript and many constructive comments.

Funding

This study was funded by TÜBİTAK (The Scientific and Technological Research Council of Turkey, Grant Number 112T418).

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Authors and Affiliations

  1. Vocational School of Health Services, Sivas Cumhuriyet University, Sivas, 58140, Türkiye

    Özgül Doğan

  2. Department of Bioinformatics, Institute of Science, Sivas Cumhuriyet University, Sivas, 58140, Türkiye

    Mahir Budak

  3. Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, 58140, Türkiye

    Mahir Budak, Melissa Şafak Salman & Ertan Mahir Korkmaz

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  1. Özgül Doğan
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  2. Mahir Budak
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Contributions

OD contributed to the generation and interpretation of data and edited the manuscript. MB performed the analyses and contributed to interpretation of data. MŞS contributed to the generation of data and edition of the manuscript. EMK involved in the conceptualization, supervision, final interpretation of data, and editing of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Ertan Mahir Korkmaz.

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The authors declare no competing interests.

Ethical approval

Research procedures in this study did not violate any relevant laws and regulations. No relevant ethics committee(s) or institution(s) were applicable for the materials used in this study.

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Edited by Sassan Asgari

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Supplementary Information

Below is the link to the electronic supplementary material.

11262_2024_2050_MOESM1_ESM.pdf

Homologous repeats (hrs) of NeseNPV-TR. The late/very late promoter motif (A/G/T)TAAG and the potential GATA factor binding site are underlined with red and then boxed, respectively. Supplementary file1 (PDF 1514 KB)

11262_2024_2050_MOESM2_ESM.pdf

Phylogenetic tree of baculoviruses constructed under ML approach using the dataset of combination of the 38 core genes and polh/gran genes. Culex nigripalpus NPV (deltabaculovirus) used as outgroup. Only bootstrap values lower than 100 in ML were shown. Supplementary file2 (PDF 4753 KB)

11262_2024_2050_MOESM3_ESM.pdf

Phylogenetic tree of baculoviruses constructed under BI approach using the dataset of combination of the 38 core genes and polh/gran genes. Culex nigripalpus NPV (deltabaculovirus) used as outgroup. Only support values lower than 1.0 in BI were shown. Supplementary file3 (PDF 6250 KB)

Supplementary file4 (XLSX 56 KB)

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Doğan, Ö., Budak, M., Salman, M.Ş. et al. Comparative genomics of the Neodiprion sertifer nucleopolyhedrovirus from Turkey with the fewest ORFs among baculoviruses. Virus Genes 60, 194–207 (2024). https://doi.org/10.1007/s11262-024-02050-1

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