In silico identification of two novel viruses on Iranian pistachio

Document Type : Short Article

Authors

1 Department of Plant Protection, Gorgan University of Agricultural Sciences and Natural Resources

2 Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran

3 Gorgan University of Agricultural Sciences and Natural Resources, Department of Plant Protection

Abstract

The pistachio is a commercial nut crop that belongs to the family Anacardiaceae. Reports for viral agents of this plant are limited to hop stunt viroid, pistachio ampelovirus A, and pistacia virus B. We investigated of the presence of viruses in Iranian Pistacia vera by analyzing publicly available RNA-Seq data. Twelve paired-end datasets were retrieved from the Sequence Read Archive (SRA) database of NCBI. Transcriptomic data were mapped to P. vera reference genome using Hisat2 to eliminate plant RNAs. The remaining data were de novo assembled by MEGAHIT and Trinity programs and the resultant contigs subsequently were queried versus viral reference sequences using BLASTx. Two novel viruses related to the family Kitaviridae were identified and tentatively named “pistachio virus x” (MT334618-20) and “pistachio virus y” (MT362605-06). Based on the genome structure, sequences similarity, and phylogenetic relationships we propose these novel viruses as possible members of genera Higrevirus and Cilevirus. High reads number on different plant tissues, root and leaf, of pistachio virus x led us to make a conclusion on possible systemic infection of this virus on Pistacia vera. To the best of our knowledge, it is the first report of possible viral agent from Iranian pistachios.

Keywords

References

Al Rwahnih M. Rowhani A. Westrick N. Stevens K. Diaz-Lara A. Trouillas FP et al. 2018. Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing. Plant Disease 102(7):1419–25.
Bolger  A. M. Lohse M. Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics btu170.
Buzkan N. Chiumenti M. Massart S. Sarpkaya K. Karadağ S. Minafra A. 2019. A new emaravirus discovered in Pistacia from Turkey. Virus Research 263:159–63.
Elleuch A. Hamdi I. Ellouze O. Ghrab M. Fkahfakh H. Drira N. 2013. Pistachio (Pistacia vera L.) is a new natural host of Hop stunt viroid. Virus Genes 47(2):330–7.
Ciuffo M. Kinoti W. M. Tiberini A. Forgia M. Tomassoli L. Constable F. E. et al. 2020. A new blunervirus infects tomato crops in Italy and Australia. Archives of Virology 165(10):2379–84.
Darriba D. Posada D. Kozlov A. M. Stamatakis A. Morel B. Flouri T. 2020. ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. Molecular Biology and Evolution 37(1):291–4.
Gilbert K. B. Holcomb E. E. Allscheid R. L. Carrington J. C. .2019. Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes. PLoS ONE 14:1–51.
Grabherr M. G. Haas B. J. Yassour M. Levin J. Z. Thompson D. A. Amit I. et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29(7):644–52.
Kim D. Paggi JM. Park C. Bennett C. Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology 37(8):907-15.
Kozlov A. M. 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(21):4453–5.
Leinonen R. Sugawara H. Shumway M. 2010. International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic acids research 39:19-21.
Li D. Liu C. M. Luo R. Sadakane K. Lam T. W. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31(10):1674–6.
Li H. Handsaker B. Wysoker A. Fennell T. Ruan J. Homer N. et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078–9.
Li H. Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25(14):1754–60.
Maddahian M. Massumi H. Heydarnejad J. Hosseinipour A. Khezri A. Sano T. 2019. Biological and molecular characterization of hop stunt viroid variants from pistachio trees in Iran. Journal of Phytopathology. 167: 163– 173.
Melzer M. J. Sether D. M. Borth W. B. Hu J. S. 2012. Characterization of a virus infecting Citrus volkameriana with citrus leprosis-like symptoms. Phytopathology, 102(1):122–7.
Nury S, Hosseini A, Gibbs AJ, Mohammadi M (2020) Poison hemlock virus Y (PHVY), a novel potyvirus from Iranian Conium maculatum (Apiaceae). Australasian Plant Pathology 49(2):119–26.
Read D. A. Muoma J. Thompson G. D. 2020. Metaviromic analysis reveals coinfection of papaya in western Kenya with a unique strain of Moroccan watermelon mosaic virus and a novel member of the family Alphaflexiviridae. Archives of Virology 165(5):1231–4.
Quito-Avila D. F. Freitas-Astúa J. Melzer M. J. 2020. Bluner-, Cile-, and Higreviruses (Kitaviridae). Reference Module in Life Sciences 1–5.
Zeng L. Tu XL. Dai H. Han FM. Lu BS. Wang M. S. et al. 2019. Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Genome Biology 20(1):1–13.
 
Iranian Journal of Plant Pathology
Volume 57, Issue 1
October 2021
Pages 81-85

Files

Share

How to cite

Statistics