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Complete genome sequence of a novel polerovirus infecting chickpea (Cicer arietinum L.)

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Abstract

The complete genome sequence of a novel polerovirus identified in chickpea (C. arietinum L.) is presented. Its sequence was assembled using small RNA sequencing and assembly (sRSA) and confirmed by RT-PCR, 5' and 3’ RACE, and Sanger sequencing. According to the current ICTV sequence demarcation criterion of greater than 10% amino acid (aa) sequence divergence in all gene products when compared to other poleroviruses, the newly identified polerovirus should be classified as a member of a new species, and we propose the name "chickpea leafroll virus" (CpLRV) for this virus. The genome of CpLRV is 5,770 nucleotides (nt) long and is organized into seven open reading frames (ORFs), designated as ORF0, ORF1, ORF2, ORF3a, ORF3, ORF4, and ORF5, which code for putative P0, P1, P1-P2, P3a, P3, P4, and P3-P5 proteins, respectively. The 5’ untranslated region (UTR) consists of 27 nt, starting with the conserved sequence 5′-ACAAAA-3′, which is typical of poleroviruses, while the 3′ UTR consists of 229 nt. Phylogenetic analysis based on the aa sequences of P0, P1, P1-P2, P3, P4, and P3-P5 showed that CpLRV clustered with members of the genus Polerovirus and is closely related to chickpea chlorotic stunt virus (CpCSV) and faba bean polerovirus 1 (FBPV1). Recombination analysis suggested that CpLRV is a recombinant of two unknown viruses that share the highest nucleotide sequence similarity with FBPV1 (76.9% identity) and suakwa aphid-borne yellows virus (SAbYV) (64.8% identity). The putative recombination event was identified in the 5’ region of the CpLRV genome, the region that encodes proteins P0, P1, and P1–P2. This is the first report of a polerovirus infecting chickpea in Mexico.

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References

  1. Servicio de Información Agroalimentaria y Pesquera (SIAP) Panorama Agroalimentario (2021) On line: https://nube.siap.gob.mx/gobmx_publicaciones_siap/pag/2021/Panorama-Agroalimentario-2021. Accessed on April 7th, 2022

  2. Chatzivassiliou EK (2021) An annotated list of legume-infecting viruses in the light of metagenomics. Plants 10(7):1413

    Article  Google Scholar 

  3. Sõmera M, Fargette D, Hébrard E, Sarmiento C, Consortium IR (2021) ICTV Virus Taxonomy Profile: Solemoviridae 2021. J Gen Virol 102(12):001707

    Article  Google Scholar 

  4. Brault V, Herrbach É, Reinbold C (2007) Electron microscopy studies on luteovirid transmission by aphids. Micron 38:302–312

    Article  CAS  Google Scholar 

  5. Delfosse VC, Barrios-Barón MP, Distéfano AJ (2021) What we know about poleroviruses: Advances in understanding the functions of polerovirus proteins. Plant Pathol 70(5):1047–1061

    Article  Google Scholar 

  6. Pazhouhandeh M, Dieterle M, Marrocco K, Lechner E, Berry B, Brault V, Hemmer O, Kretsch T, Richards KE, Genschik P, Ziegler-Graff V (2006) F-box-like domain in the polerovirus protein P0 is required for silencing suppressor function. P Natl Acad Sci USA 103(6):1994–1999

    Article  CAS  Google Scholar 

  7. Prüfer D, Kawchuk L, Monecke M, Nowok S, Fischer R, Rohde W (1999) Immunological analysis of potato leafroll luteovirus (PLRV) P1 expression identifies a 25 kDa RNA-binding protein derived via P1 processing. Nucleic Acids Res 27(2):421–425

    Article  Google Scholar 

  8. Prüfer D, Tacke E, Schmitz J, Kull B, Kaufmann A, Rohde W (1992) Ribosomal frameshifting in plants: A novel signal directs the – 1 Frameshift in the Synthesis of the Putative Viral Replicase of Potato Leafroll Luteovirus. EMBO J 11(3):1111–1117

    Article  Google Scholar 

  9. Nixon PL, Rangan A, Kim YG, Rich A, Hoffman DW, Hennig M, Giedroc DP (2002) Solution structure of a Luteoviral P1-P2 frameshifting mRNA pseudoknot. J Mol Biol 322:621–633

    Article  CAS  Google Scholar 

  10. Cornish PV, Hennig M, Giedroc DP (2005) A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated – 1 ribosomal frameshifting. P Natl Acad Sci 102(36):12694–12699

    Article  CAS  Google Scholar 

  11. Smirnova E, Firth AE, Miller WA, Scheidecker D, Brault V, Reinbold C, Rakotondrafara AM, Chung BYW, Ziegler-Graff V (2015) Discovery of a small non-AUG-initiated ORF in poleroviruses and luteoviruses that is required for long-distance movement. PLoS Pathog 11(5):e1004868

    Article  Google Scholar 

  12. Ziegler-Graff V, Brault V, Mutterer JD, Simonis MT, Herrbach E, Guilley H, Richards KE, Jonard G (1996) The coat protein of beet western yellows luteovirus is essential for systemic infection but the viral gene products P29 and P19 are dispensable for systemic infection and aphid transmission. Mol Plant Microbe Interact 9(6):501–510

    Article  CAS  Google Scholar 

  13. Schmitz J, Stussi-Garaud C, Tacke E, Prüfer D, Rohde W, Rohfritsch O (1997) In situ localization of the putative movement protein (pr17) from potato leafroll luteovirus (PLRV) in infected and transgenic potato plants. Virology 235:311–322

    Article  CAS  Google Scholar 

  14. Brown CM, Dinesh-Kumar SP, Miller WA (1996) Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon. J Virol 70:5884–5892

    Article  CAS  Google Scholar 

  15. Bruyère A, Brault V, Ziegler-Graff V, Simonis MT, Van den Heuvel J, Richards K, Guilley H, Jonard G, Herrbach E (1997) Effects of mutations in the beet western yellows virus readthrough protein on its expression and packaging and on virus accumulation, symptoms, and aphid transmission. Virology 230:323–334

    Article  Google Scholar 

  16. Pagán I, Holmes EC (2010) Long-term evolution of the Luteoviridae: time scale and mode of virus speciation. J Virol 84:6177–6187

    Article  Google Scholar 

  17. Chiquito-Almanza E, Acosta-Gallegos JA, García-Álvarez NC, Garrido-Ramírez ER, Montero-Tavera V, Guevara-Olvera L, Anaya-López JL (2017) Simultaneous detection of both RNA and DNA viruses infecting dry bean and occurrence of mixed infections by BGYMV, BCMV and BCMNV in the Central-west region of Mexico. Viruses 9(4):63

    Article  Google Scholar 

  18. Zheng Y, Gao S, Padmanabhan C, Li R, Galvez M, Gutierrez D, Fuentes S, Ling KS, Kreuze J, Fei Z (2017) VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology 500:130–138

    Article  CAS  Google Scholar 

  19. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359

    Article  CAS  Google Scholar 

  20. Giedroc DP, Theimer CA, Nixon PL (2000) Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol 298(2):167–185

    Article  CAS  Google Scholar 

  21. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  Google Scholar 

  22. Martin DP, Varsani A, Roumagnac P, Botha G, Maslamoney S, Schwab T, Kelz Z, Kumar V, Murrell B (2021) RDP5: A computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets. Virus Evol 7(1):veaa087

    Article  Google Scholar 

  23. Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9(9):e108277

    Article  Google Scholar 

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Acknowledgments

This study was funded by INIFAP project no. 10371234370.

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  1. Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío, km 6.5 carretera Celaya-San Miguel de Allende S/N. C.P. 38110, Celaya, Gto, México

    E. Chiquito-Almanza, J. A. Acosta-Gallegos & J. L. Anaya-López

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  1. E. Chiquito-Almanza
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  2. J. A. Acosta-Gallegos
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  3. J. L. Anaya-López
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Correspondence to J. L. Anaya-López.

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Chiquito-Almanza, E., Acosta-Gallegos, J.A. & Anaya-López, J.L. Complete genome sequence of a novel polerovirus infecting chickpea (Cicer arietinum L.). Arch Virol 167, 2783–2788 (2022). https://doi.org/10.1007/s00705-022-05581-w

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