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Whole-genome sequencing and comparative transcriptome analysis of Bombyx mori nucleopolyhedrovirus La strain

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Abstract

The Bombyx mori nucleopolyhedrovirus (BmNPV) La is a variant BmNPV strain isolated in Laos. La has different features from BmNPV type strain T3 in virulence, production of the polyhedrin protein, and the formation of multicapsid occlusion-derived viruses. Here, the whole-genome sequence of La was compared to the sequences of nine BmNPV and two Bombyx mandarina nucleopolyhedrovirus strains. The complete La genome consisted of 127,618 base pairs with a G + C content of 40.3% and contained putative 136 open reading frames encoding more than 60 amino acids. The La genome lacked the bro-b gene and had the highest identity with that of the T3 strain. A comparison of the transcriptomes of La- and T3-infected cells showed that the expression levels of the polyhedrin and cathepsin genes were greater in cells infected with La as compared to those infected with T3. Interestingly, the virus genes with different RNA levels between the two BmNPV strains were assembled into five clusters in the genome of La. Also, the RNA levels of host ribosomal protein genes were significantly decreased in cells infected with La as compared to those infected with T3.

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Acknowledgements

This work was supported by Grants from JSPS KAKENHI (Grant No. 19J13817) and Young Innovation Scholarship of Utsunomiya University to SF, MEXT KAKENHI (Grant No. 221S0002) to YS, JSPS KAKENHI (Grant Nos. 25292196, 16H05051, 19H02966) to SK, and Venture Business Laboratory Program F of Utsunomiya University and A-step Feasibility Study Program of the Japan Science and Technology Agency (Grant No. AS262Z01406N) to MI. The authors would like to thank Enago (www.enago.jp) for the English language review.

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  1. Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya-shi, Tochigi, 321-8505, Japan

    Shota Fujimoto, Keisuke Shoji & Masashi Iwanaga

  2. Department of Biological Production Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwai 3-5-8, Fuchu-shi, Tokyo, 183-8509, Japan

    Shota Fujimoto & Masashi Iwanaga

  3. Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan

    Munetaka Kawamoto & Susumu Katsuma

  4. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan

    Yutaka Suzuki

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All authors contributed to the study conception and design. The experiments were conceived and designed by Shota Fujimoto and Masashi Iwanaga. The experiments were performed by Shota Fujimoto, Munetaka Kawamoto, Keisuke Shoji, Yutaka Suzuki, Susumu Katsuma, and Masashi Iwanaga. The paper was written by Shota Fujimoto, Susumu Katsuma, and Masashi Iwanaga.

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11262_2019_1727_MOESM1_ESM.pptx

Supplementary file1 (PPTX 844 kb)—Fig. S1 Validation of differential virus gene expression levels between La and T3. BmN cells were inoculated with BmNPV La or T3 and total RNA was purified at 72 and 96 hpi. The RNA levels of representative virus genes contained within clusters A to E were analyzed by RT-qPCR. The results are presented as the average of three independent experiments. The error bars indicate standard deviations. The asterisks indicate significant differences (Student’s t-test, *p < 0.05, **p < 0.01, ***p < 0.005). Fig. S2 Validation of MA plot analysis between La- and T3-infected cells. (a) Genes that were abundantly transcribed (A > 6) with lower RNA levels in cells infected with La as compared to those infected with T3. (b) Genes that were abundantly transcribed (A > 6) with the same RNA levels in La- and T3-infected cells. BmN cells infected with La or T3 were collected at 72 and 96 hpi, and total RNA was purified and subjected to RT-qPCR analysis. The results are presented as the average of three independent experiments. The error bars indicate standard deviations. The asterisks indicate significant differences (Student’s t-test, *p < 0.05, ***p < 0.005)

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Fujimoto, S., Kawamoto, M., Shoji, K. et al. Whole-genome sequencing and comparative transcriptome analysis of Bombyx mori nucleopolyhedrovirus La strain. Virus Genes 56, 249–259 (2020). https://doi.org/10.1007/s11262-019-01727-2

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