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Complete genome sequences of two novel dicistroviruses detected in yellow crazy ants (Anoplolepis gracilipes)

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A Correction to this article was published on 02 September 2020

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Abstract

We report two novel RNA viruses from yellow crazy ants, (Anoplolepis gracilipes) detected using next-generation sequencing. The complete genome sequences of the two viruses were 10,662 and 8,238 nucleotides in length, respectively, with both possessing two open reading frames with three conserved protein domains. The genome organization is characteristic of members of the genus Triatovirus in the family Dicistroviridae. The two novel viruses were tentatively named “Anoplolepis gracilipes virus 1” and “Anoplolepis gracilipes virus 2” (AgrV-1 and AgrV-2). Phylogenetic analyses based on amino acid sequences of the non-structural polyprotein (ORF1) suggest that the two viruses are triatovirus-like viruses. This is the first report on the discovery of novel triatovirus-like viruses in yellow crazy ants with a description of their genome structure (two ORFs and conserved domains of RNA helicase, RNA-dependent RNA polymerase, and capsid protein), complete sequences, and viral prevalence across the Asia-Pacific region.

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Fig. 1
Fig. 2

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Data availability

All viral sequences in this article are publicly available (GenBank accession numbers: MT108239 and MT108240) and also available as supplementary materials.

Change history

  • 02 September 2020

    Authors would like to correct the error in Fig. 1 which was incorrectly updated in the original publication.

References

  1. Valles SM, Chen Y, Firth AE, Guérin DM, Hashimoto Y, Herrero S, de Miranda JR, Ryabov E (2017) ICTV virus taxonomy profile: dicistroviridae. J Gen Virol 98:355–356

    Article  CAS  Google Scholar 

  2. Kleanthous E, Olendraite I, Lukhovitskaya NI, Firth AE (2019) Discovery of three RNA viruses using ant transcriptomic datasets. Arch Virol 164:643–647

    Article  CAS  Google Scholar 

  3. Valles SM, Rivers AR (2019) Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range. Virus Genes 55:368–380

    Article  CAS  Google Scholar 

  4. Viljakainen L, Holmberg I, Abril S, Jurvansuu J (2018) Viruses of invasive Argentine ants from the European Main supercolony: characterization, interactions and evolution. J Gen Virol 99:1129–1140

    Article  CAS  Google Scholar 

  5. Reuter G, Pankovics P, Gyöngyi Z, Delwart E, Boros Á (2014) Novel dicistrovirus from bat guano. Arch Virol 159:3453–3456

    Article  CAS  Google Scholar 

  6. Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J (2016) Redefining the invertebrate RNA virosphere. Nature 540:539–543

    Article  CAS  Google Scholar 

  7. Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H, Hingamp P, Goto S, Ogata H (2016) Linking virus genomes with host taxonomy. Viruses 8:66

    Article  Google Scholar 

  8. Payne AN, Shepherd TF, Rangel J (2020) The detection of honey bee (Apis mellifera) associated viruses in ants. Sci Rep 10:2923

    Article  CAS  Google Scholar 

  9. Cooling M, Gruber MAM, Hoffmann BD, Sébastien A, Lester PJ (2017) A metatranscriptomic survey of the invasive yellow crazy ant, Anoplolepis gracilipes, identifies several potential viral and bacterial pathogens and mutualists. Insect Soc 64:197–207

    Article  Google Scholar 

  10. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  Google Scholar 

  11. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  Google Scholar 

  12. Buchfink B, **e C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60

    Article  CAS  Google Scholar 

  13. Huson D, Beier S, Flade I, Gorska A, El-Hadidi M, Mitra S, Ruscheweyh H, Rewati Tappu D (2016) MEGAN community edition—interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol 12:e1004957

    Article  Google Scholar 

  14. Rombel IT, Sykes KF, Rayner S, Johnston SA (2002) ORF-FINDER: a vector for high-throughput gene identification. Gene 282:33–41

    Article  CAS  Google Scholar 

  15. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH (2015) CDD: NCBI’s conserved domain database. Nucleic Acids Res 43:D222–D226

    Article  CAS  Google Scholar 

  16. Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T (2020) ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol Biol Evol 37:291–294

    Article  CAS  Google Scholar 

  17. Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A (2019) RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453–4455

    Article  CAS  Google Scholar 

  18. Letunic I, Bork P (2019) Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47:W256–W259

    Article  CAS  Google Scholar 

  19. Yang CC, Yu YC, Valles SM, Oi DH, Chen YC, Shoemaker DW, Wu WJ, Shih CJ (2010) Loss of microbial (pathogen) infections associated with recent invasions of the red imported fire ant Solenopsis invicta. Biol Invasions 12:3307–3318

    Article  Google Scholar 

  20. Culley AIL, Suttle CA (2012) Family dicistroviridae. In: King AMQA, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy, classification and nomenclature of viruses. 9th report of the ICTV Elsevier Academic Press, Amsterdam, pp 840–854

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Acknowledgements

We would like to express our sincere gratitude to the Research Institute for Sustainable Humanosphere, Kyoto University and the Environment Research and Ministry of the Environment, Japan, for financial support. We also extend our appreciation to Kazuki Tsuji, Chung-Chi Lin, Chow-Yang Lee, Ching-Chen Lee, Hui-Siang Tee, Mark Ooi, and Zhengwei Jong for field assistance, as well as three anonymous reviewers for constructive comments on earlier versions of the manuscript.

Funding

This research was financially supported by the Research Institute for Sustainable Humanosphere, Kyoto University and the Environment Research and Technology Development Fund, the Ministry of the Environment, Japan.

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Author notes

  1. Chih-Chi Lee, Chun-Yi Lin and Hung-Wei Hsu contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan

    Chih-Chi Lee & Hung-Wei Hsu

  2. Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, 611-0011, Japan

    Chun-Yi Lin & Chin-Cheng Scotty Yang

  3. Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA

    Chin-Cheng Scotty Yang

  4. Department of Entomology, National Chung Hsing University, Taichung, 402204, Taiwan

    Chin-Cheng Scotty Yang

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  1. Chih-Chi Lee
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  2. Chun-Yi Lin
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  3. Hung-Wei Hsu
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  4. Chin-Cheng Scotty Yang
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Contributions

C-CL: virus genome assembly, annotation, phylogenetic analysis, manuscript preparation. C-YL: RNA preparation, high throughput sequencing, manuscript preparation. H-WH: primer design, RT-PCR, and wet lab work. C-CSY: supervising all work, providing advice, securing funding, manuscript preparation.

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Correspondence to Chin-Cheng Scotty Yang.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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The original version of this article was revised: Correct version of figure 1 updated here.

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Lee, CC., Lin, CY., Hsu, HW. et al. Complete genome sequences of two novel dicistroviruses detected in yellow crazy ants (Anoplolepis gracilipes). Arch Virol 165, 2715–2719 (2020). https://doi.org/10.1007/s00705-020-04769-2

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  • DOI: https://doi.org/10.1007/s00705-020-04769-2

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