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Genetic diversity of the coat protein gene and biological variation of citrus yellow vein clearing virus infecting different citrus species

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Abstract

Citrus is one of the most important fruit crops globally and rising incidence of citrus yellow vein clearing virus (CYVCV) in citrus orchards is an increasing concern in India. CYVCV and Indian citrus ringspot virus (ICRSV) are assigned to the only two known species in the genus Mandarivirus. Both viruses naturally infect several citrus plants. ICRSV produces ringspots symptoms in Kinnow mandarin, whereas CYVCV induces vein clearing symptoms on Etrog citron and lemon. Leaf samples and bud sticks of different citrus cultivars, exhibiting diverse symptoms were collected during 2012–2014 from 18 locations of India. The genetic variability was assessed through analysis of the coat protein (CP) gene sequences. Out of the 15 CP gene sequences, 13 sequences were of 978 nucleotides (nts) and showed 96–99% sequence identity with CYVCV-Y1 isolate (JX040635.1). However, sequences from the isolates HI and DLI shared only 78% and 73% nucleotide sequence identity with CYVCV and ICRSV, respectively, and that may represent distinct CYVCV isolates in the genus Mandarivirus. In phylogenetic analysis also HI and DLI isolates clustered neither with CYVCV nor with ICRSV isolates.

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Acknowledgments

The authors are thankful to the head, Division of Plant Pathology, Director, Indian Agricultural Research Institute for necessary lab facilities and ICAR Outreach programme for financial support. We are grateful to Dr. Susheel Sharma and Dr. Sandeep Raheja for help rendered in sample collection. The first author is indebted to Indian council of Agricultural Research, New Delhi for availing study leave during his PhD research programme.

Funding

The author(s) received the financial support under the ICAR- OUTREACH programme for the research work.

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Authors

Contributions

The first author Ram Prasnna Meena, study conception and acquisition of data, bioassay other field works and drafting of manuscript. The corresponding author V. K. Baranwal devised the experiment, proper monitoring and analysing the sequences and did critical revision of drafted manuscript.

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Correspondence to V. K. Baranwal.

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Supplementary Fig. 1

The two-dimensional colour-coded graphical represented the “Percent identities of the complete coat protein amino acid sequences of CYVCV, ICRSV and related genera, are shown above the diagonal, and percent nucleotide identity below the diagonal. A scale with the percent colour code is presented for similarity indexing. *Accession numbers of keys used in as 1–56 numbers: 1. JX040635.1 VC Y1; 2. KX156752.1 VC YN-NH; 3. KX156751.1 VC YN-EL; 4. KX156734.1 VC YN-SA; 5. KT696511.1 VC RMGI; 6. KX156746.1 VC JX-NF; 7. KX156742.1 VC GX-STJ; 8. KX156735.1 VC CQ-PO; 9. KT696513.1 VC KPMI; 10. KT696512.1 VC PALI; 11. KX156750.1 VC YN-BTC; 12. KX156745.1 VC HN-STJ; 13. KX156744.1 VC HN-GXP; 14. KX156743.1 VC GZ-GXP; 15. KX156738.1 VC GD-JG; 16. KX156737.1 VC FJ-PK; 17. KT345342.1 VC IS; 18. KT696515.1 VC LKI; 19. KT696522.1 VC DLI; 20. KX156741.1 VC GX-GXP; 21. KX156739.1 VC GD-STJ; 22. KX156736.1 VC CQ-TA; 23. KX378154.1 VC JX; 24. KT124646.1 VC HU; 25. KT696516.1 VC KLI; 26. KX156747.1 VC JX-NH; 27. KP313240.1 VC CQ; 28. KT696520.1 VC FRBI; 29. KT696518.1 VC FKI; 30. KT696517.1 VC AKI; 31. KX156740.1 VC GD-STP; 32. KY933794.1 VC ZJ_1; 33. KX156749.1 VC SC-NH; 34. KX156748.1 VC SC-EL; 35. KY933797.1 VC ZJ_4; 36. KT696519.1 VC SMI; 37. KT696514.1 VC AEI; 38. KP313242.1 VC YN; 39. MG878869.1 VC AY204; 40. KY933796.1 VC ZJ_3; 41. KY933795.1 VC ZJ_2; 42. KP313241.1 VC PK; 43. KP120977.1 VC-RL; 44. AY255007.1 RS Ahm; 45. KT696510.1 VC ECAI; 46. AY255008.1 RS Pune; 47. KT696521.1 VC ALI; 48. KT696523.1 – HI; 49. KT696524.1- DLI2; 50. KT696525.1 RS KPI; 51. HQ324250.1 RS Pune; 52. AY255006.1 RS Delhi; 53. AF406744.1 RS; 54. AF184962.1 RS; 55. AY255009. RS Ab; 56. M31541.1 PVX. (JPG 1410 kb)

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Meena, R.P., Baranwal, V.K. Genetic diversity of the coat protein gene and biological variation of citrus yellow vein clearing virus infecting different citrus species. Trop. plant pathol. 45, 467–475 (2020). https://doi.org/10.1007/s40858-020-00333-0

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