Skip to main navigation menu Skip to main content Skip to site footer
Plant Science Today (PST)

Research Articles

Early Access

Virome profiling of pigeonpea using high-throughput sequencing and development of LAMP assay for PPSMV detection

DOI
https://doi.org/10.14719/pst.12974
Submitted
28 November 2025
Published
25-02-2026

Abstract

Pigeonpea (Cajanus cajan (L.) Millsp) is a major pulse crop vulnerable to various biotic stresses including viral diseases. In addition to known viruses, novel and emerging viruses further threaten its production. In the current study, a survey was conducted in pigeonpea fields of Karnataka, India during 2023-24. The incidence of pigeonpea viral diseases in the surveyed areas ranged from 2 to 34 %. During the survey thirty virus infected pigeonpea samples were collected for virome analysis. Total RNA extracted from fifteen samples each from Northern and Southern Karnataka was pooled separately into two equimolar RNA samples and subjected to virome profiling. The rRNA-depleted RNA was used to prepare mRNA libraries, which were sequenced on the Illumina NovaSeq 6000 platform. Virome analyses revealed the presence of three different viruses: pigeonpea sterility mosaic virus 1 (PPSMV 1), pigeonpea sterility mosaic virus 2 (PPSMV 2) and horsegram yellow mosaic virus (HgYMV) from Northern Karnataka and only PPSMV 1 from Southern Karnataka. Sequencing was validated by reverse transcription polymerase chain reaction (RT-PCR) in individual samples, which revealed the prevalence of PPMSV 1, PPMSV 2 and HgYMV in Karnataka, India. Further, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) diagnostic assay was developed to detect PPMSV, which can be used for routine detection. Among the identified viruses in pigeonpea, HgYMV is reported for the first time from Karnataka, India.

References

  1. 1. Shirsat MS, Thomas B, Niji MS, Kumar AS. Growing healthy vegetables: A scientific approach. In: Varun BH, Sahu SK, Gautham SP, Akshita B, Sheetal R, editors. Advancements in pigeon pea (Cajanus cajan L. Millsp.) cultivation and breeding in India. 1st ed. Haryana: Paper Trail Publication; 2025. p. 113.
  2. 2. FAOSTAT. Food and Agriculture Organization of the United Nations Statistical Database. Rome: FAO; 2023. Available from: http://www.fao.org/faostat/en/#data/QC
  3. 3. Sayiprathap BR, Patibanda AK, Mantesh M, Hiremath S, Sagar N, Reddy CL, et al. Sterility mosaic disease of pigeonpea (Cajanus cajan (L.) Huth): current status, disease management strategies and future prospects. Plants. 2024;13(15):2146. https://doi.org/10.3390/plants13152146
  4. 4. Kumar PL, Jones AT, Waliyar F. Virus diseases of pegionpea. In: Rao GP, Kumar PL, Holguin RJ, editors. Vegetable and pulse crops: Vol. 3. Characterization, diganosis and management of plant viruses. USA: Studium Press LLC. 2008. p. 235–57.
  5. 5. Jones AT, Kumar PL, Saxena KB, Kulkarni NK, Muniyappa V, Waliyar F. Sterility mosaic disease-the “green plague” of pigeonpea: Advances in understanding the etiology, transmission and control of a major virus disease. Plant Dis. 2004;88(5):436–45.
  6. 6. Patil BL, Kumar PL. Pigeonpea sterility mosaic virus: A legume infecting Emara virus from South Asia. Mol Plant Pathol. 2015;16(8):775–86. https://doi.org/10.1111/mpp.12238
  7. 7. Kulkarni NK, Kumar PL, Muniyappa V, Jones AT, Reddy DVR. Transmission of pigeonpea sterility mosaic virus by the eriophyid mite Aceria cajani (Acari: Arthropoda). Plant Dis. 2002;86:1297–302. https://doi.org/10.1094/PDIS.2002.86.12.1297
  8. 8. Elbeaino T, Digiaro M, Uppala M, Sudini H. Deep sequencing of dsRNAs recovered from mosaic-diseased pigeonpea reveals the presence of a novel Emara virus: Pigeonpea sterility mosaic virus 2. Arch Virol. 2015;160(8):2019–29. https://doi.org/10.1007/s00705-015-2479-y
  9. 9. Newton W, Peiris J. Virus diseases of plants in Ceylon. FAO Plant Prot Bull. 1953;2(2):17–21.
  10. 10. Williams F, Grewal J, Amin K. Serious and new diseases of pulse crops in India in 1966. Plant Dis Rep. 1968;52(4):300–304.
  11. 11. Akram M, Kumar D, Saurav S, Saxena M, Saxena DR, Kamaal N, et al. Molecular characterization of yellow mosaic disease-causing begomoviruses in pigeonpea (Cajanus cajan L.) from three agroecological zones of India. Curr Microbiol. 2025;82(2):95. https://doi.org/10.1007/s00284-025-04080-w
  12. 12. Rubio L, Galipienso L, Ferriol I. Detection of plant viruses and disease management: Relevance of genetic diversity and evolution. Front Plant Sci. 2020;11:1092. https://doi.org/10.3389/fpls.2020.01092
  13. 13. Wassenegger M. Advantages and disadvantages of using PCR techniques to characterize transgenic plants. Mol Biotechnol. 2001;17(1):73–82. https://doi.org/10.1385/MB:17:1:73
  14. 14. Maina S, Jones RA. Enhancing biosecurity against virus disease threats to Australian grain crops: Current situation and future prospects. Front Hortic. 2023;2:1263604. https://doi.org/10.3389/fhort.2023.1263604
  15. 15. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28(12):e63. https://doi.org/10.1093/nar/28.12.e63
  16. 16. Jose S, Radhika NS. Key viruses of pulses in Australia: General detection and management methods. Int J Plant Soil Sci. 2025;37(5):389–98. https://doi.org/10.9734/ijpss/2025/v37i55462
  17. 17. Ibaba JD, Gubba A. High-throughput sequencing application in the diagnosis and discovery of plant-infecting viruses in Africa, a decade later. Plants. 2020;9(10):1376. https://doi.org/10.3390/plants9101376
  18. 18. Jegadeesan S, Raizada A, Dhanasekar P, Suprasanna P. Draft genome sequence of the pulse crop blackgram (Vigna mungo (L.) Hepper) reveals potential R-genes. Sci Rep. 2021;11(1):11247. https://doi.org/10.1038/s41598-021-90683-9
  19. 19. Sudha M, Karthikeyan A, Madhumitha B, Veera Ranjani R, Mathivathana MK, Dhasarathan M, et al. Dynamic transcriptome profiling of mungbean genotypes unveils genes responding to mungbean yellow mosaic virus infection. Pathogens. 2022;11(2):190. https://doi.org/10.3390/pathogens11020190
  20. 20. Jha UC, Nayyar H, Sharma KD, Jha R, Thudi M, Bakır M, et al. Chickpea diseases: breeding and “omics” approaches for designing next-generation disease-resistant chickpea cultivars. In: Jha UC, editor. Diseases in legume crops. Singapore: Springer Nature; 2023. p. 1–30. https://doi.org/10.1007/978-981-99-3358-7_1
  21. 21. Wheeler BE. An introduction to plant diseases. London: Wiley; 1969. p. 374.
  22. 22. Tejaswi K, Reddy BB, Prasanthi L, Pradeep M. Survey for the occurrence of yellow mosaic disease in major pigeonpea growing areas in Andhra Pradesh. Agric Sci. 2023;11(1):64–67.
  23. 23. Sajeevan RS, Shivanna MB, Nataraja KN. An efficient protocol for total RNA isolation from healthy and stressed tissues of mulberry (Morus sp.) and other species. Am J Plant Sci. 2014;5:2057–65.
  24. 24. Karadi A, Samineni S, Sajja S, Sharma M, Thudi M, Mallikarjuna BP, et al. Molecular mapping of dry root rot resistance genes in chickpea (Cicer arietinum L.). Euphytica. 2021;217(6):123. https://doi.org/10.1007/s10681-021-02854-4
  25. 25. Andrews S. FastQC: A quality control tool for high throughput sequence data. Babraham Bioinformatics; 2010. p. 370.
  26. 26. Krueger F. Trim Galore!: A wrapper around Cutadapt and FastQC. Babraham Institute; 2015. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
  27. 27. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–52. https://doi.org/10.1038/nbt.1883
  28. 28. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: Architecture and applications. BMC Bioinformatics. 2009;10(1):421. https://doi.org/10.1186/1471-2105-10-421
  29. 29. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–48. https://doi.org/10.1093/bioinformatics/btm404
  30. 30. Hall T. BioEdit: An important software for molecular biology. GERF Bull Biosci. 2011;2(1):60–61.
  31. 31. Muhire BM, Varsani A, Martin DP. SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One. 2014;9(9):e108277. https://doi.org/10.1371/journal.pone.0108277
  32. 32. Tamura K, Stecher G, Kumar S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38:3022–27. https://doi.org/10.1093/molbev/msab120
  33. 33. Martin DP, Varsani A, Roumagnac P, Botha G, Maslamoney S, Schwab T, et al. RDP5: A computer program for analyzing recombination in and removing signals of recombination from nucleotide sequence datasets. Virus Evol. 2020;7(1):veaa087. https://doi.org/10.1093/ve/veaa087
  34. 34. Mediga KR, Sunkad G, Shil S, Kulkarni S, Patil B, Chandran US, et al. Assessment of the spatial distribution and identification of potential risk areas for sterility mosaic disease of pigeonpea (Cajanus cajan L. Huth) in southern India. Front Sustain Food Syst. 2024;8:1386823. https://doi.org/10.3389/fsufs.2024.1386823
  35. 35. Netla VR, Hiremath S, Muttappagol M, Kumar HDV, Prasanna SK, Kumar TM, et al. Virome analysis of field-collected chilli samples reveals diverse viruses. Virol J. 2025;22(1):116. https://doi.org/10.1186/s12985-025-02713-x
  36. 36. Chai M, Ma X, Chang S, Cheng X. Isolation of double-stranded RNAs by lithium chloride fractionation. In: Walker JM, editor. Double stranded RNA: Methods and protocols. New York: Springer US; 2024. p. 1–5. https://doi.org/10.1007/978-1-0716-3702-9_1
  37. 37. Gaafar YZ, Herz K, Hartrick J, Fletcher J, Blouin AG, MacDiarmid R, et al. Investigating the pea virome in Germany: Old friends and new players in the field(s). Front Microbiol. 2020;11:583242. https://doi.org/10.3389/fmicb.2020.583242
  38. 38. Rashid S, Wani F, Ali G, Sofi TA, Dar ZA, Hamid A. Viral meta transcriptomic approach to study virus diversity associated with common bean (Phaseolus vulgaris L.) in north-western Himalayan India. Front Microbiol. 2022;13:943382. https://doi.org/10.3389/fmicb.2022.943382
  39. 39. Anupama S, Netla VR, Kumar HV, Hiremath S, Muttappagol M, Prasanna SK, et al. Metaviromic analysis of cucumber reveals diverse viral infections and development of LAMP assays for rapid detection. Physiol Mol Plant Pathol. 2025;140:102900. https://doi.org/10.1016/j.pmpp.2025.102900
  40. 40. Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. The pepper virome: Natural co-infection of diverse viruses and their quasispecies. BMC Genomics. 2017;18(1):453. https://doi.org/10.1186/s12864-017-3838-8
  41. 41. Massart S, Chiumenti M, De Jonghe K, Glover R, Haegeman A, Koloniuk I, et al. Virus detection by high-throughput sequencing of small RNAs: Large-scale performance testing of sequence analysis strategies. Phytopathology. 2019;109(3):488–97. https://doi.org/10.1094/PHYTO-02-18-0067-R
  42. 42. Froissart R, Roze D, Uzest M, Galibert L, Blanc S, Michalakis Y. Recombination every day: Abundant recombination in a virus during a single multicellular host infection. PLoS Biol. 2005;3(3):e89. https://doi.org/10.1371/journal.pbio.0030089
  43. 43. Aaziz R, Tepfer M. Recombination in RNA viruses and in virus-resistant transgenic plants. J Gen Virol. 1999;80(6):1339–46.
  44. 44. Pita JS, Morris V, Roossinck MJ. Mutation and recombination frequencies reveal a biological contrast within strains of cucumber mosaic virus. J Virol. 2015;89(13):6817–23. https://doi.org/10.1128/JVI.00040-15
  45. 45. Shahid MS, Al-Sadi AM. Molecular characterization of mungbean yellow mosaic India virus infecting Vigna radiata in Oman. J Phytopathol. 2024;172(1):e13270. https://doi.org/10.1111/jph.13270
  46. 46. Rienzie R, De Costa D, Wickramaarachchi T. Transmission and host range of horsegram yellow mosaic virus causing common bean (Phaseolus vulgaris L.) yellowing disease in Sri Lanka. J Natl Sci Found Sri Lanka. 2020;48(1):81-92. https://doi.org/10.4038/jnsfsr.v48i1.8704
  47. 47. Chaithanya BH, Reddy BB, Prasanthi L, Devi RS. Molecular characterization of virus species causing yellow mosaic disease of redgram. Econ Environ Conserv. 2022;28:300–305. https://doi.org/10.53550/EEC.2022.v28i03s.045
  48. 48. Varma A, Malathi VG. Emerging geminivirus problems: A serious threat to crop production. Ann Appl Biol. 2003;142(2):145–64. https://doi.org/10.1111/j.1744-7348.2003.tb00240.x
  49. 49. Sivalingam PN, Yele Y, Sarita RK, Sharma KC. Incidence of pigeonpea yellow mosaic disease and vector population in Chhattisgarh, India. Int J Curr Microbiol Appl Sci. 2019;8:1699–703. https://doi.org/10.20546/ijcmas.2019.802.xx
  50. 50. Zidon R, Tsueda H, Morin E, Morin S. Projecting pest population dynamics under global warming: The combined effect of inter- and intra-annual variations. Ecol Appl. 2016;26(4):1198–210. https://doi.org/10.1890/15-1045

Downloads

Download data is not yet available.