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Identification and primary distribution of Citrus viroid V in citrus in Punjab, Pakistan

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Abstract

Background

Citrus plants are prone to infection by different viroids which deteriorate their vigor and production. Citrus viroid V (CVd-V) is among the six citrus viroids, belongs to genus Apscaviroid (family Pospiviroidae) which induces symptoms of mild necrotic lesions on branches and cracks on trunk portion.

Methods and results

A survey was conducted to evaluate the prevalence of CVd-V in core and non-core citrus cultivated areas of Punjab, Pakistan. A total of 154 samples from different citrus cultivars were tested for CVd-V infection by RT-PCR. The results revealed 66.66% disease incidence of CVd-V. Citrus cultivars Palestinia Sweet lime, Roy Ruby, Olinda Valencia, Kaghzi lime, and Dancy were identified as new citrus hosts of CVd-V for the first time from Pakistan. The viroid infection was confirmed by biological indexing on indicator host Etrog citron. The reported primers used for the detection of CVd-V did not amplify, rather showed non-specific amplification, which led to the designing of new primers. Whereas, new back-to-back designed primers (CVd-V AF1/CVd-V AR1) detected CVd-V successfully and obtained an expected amplified product of CVd-V with 294 bp. Sequencing analysis confirmed the new host of CVd-V showing 98–100% nucleotide sequence homology with those reported previously from other countries while 100% sequence homology to the isolates reported from Pakistan. Based on phylogenetic analysis using all CVd-V sequences in GenBank, two main CVd-V groups (I and II) were identified, and newly identified isolates during this study fall in the group I.

Conclusion

The study revealed that there are some changes in the nucleotide sequences of CVd-V which made difficult for their detection using reported primers. All isolates of Pakistan showed high sequence homology with other isolates of CVd-V from Iran and USA whereas; the isolates from China, Japan, Tunisia, and Africa are distantly related. It is evident that CVd-V is spreading in all citrus cultivars in Pakistan.

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Data availability

All data needed to conduct this study is provided within the manuscript and RNA-Seq reads have been submitted to the NCBI database under accession number given in manuscript.

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Acknowledgements

Authors thanks to the Deanship of Scientific Research, King Khalid University, Saudi Arabia for funding this work under Grant No. (RGP. 2/90/43).

Funding

The research work was partially funded by King Khalid University, Saudi Arabia under the Grant No. (RGP. 2/90/43).

Author information

Authors and Affiliations

  1. Department of Plant Pathology, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan, 60800, Punjab, Pakistan

    Amjad Ali, Ummad ud din Umar, Ateeq ur Rehman & Rashida Parveen

  2. Department of Plant Pathology, The Islamia University , Bahawalpur, Punjab, Pakistan

    Muhammad Taimoor Shakeel

  3. University of Agriculture Faisalabad, Sub Campus Burewala, Vehari, Punjab, Pakistan

    Sohail Akhtar

  4. Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, 32200, Pakistan

    Muhammad Nouman Tahir & Sagheer Atta

  5. Department of Plant Protection, Sivas University of Science and Technology, 58140, Sivas, Turkey

    Amjad Ali & Fatih Ölmez

  6. Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia

    Mahmoud Moustafa

  7. Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt

    Mahmoud Moustafa

Authors
  1. Amjad Ali
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  2. Ummad ud din Umar
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Contributions

Methodology: AA, UU and AR; software: UU, MTS, MNT and S Atta; validation: UU, SA, AR, FÖ and RP; formal analysis: AA and UU; investigation: UU, AR and RP; data curation: UU, MTS, MM and MNT; writing—original draft preparation: AA; writing—review and editing: UU, MNT, S Atta, SA, MM and FÖ; visualization: UU, AR, RP, MM and MNT; supervision: UU and AR. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Ummad ud din Umar or Ateeq ur Rehman.

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Ali, A., Umar, U., Akhtar, S. et al. Identification and primary distribution of Citrus viroid V in citrus in Punjab, Pakistan. Mol Biol Rep 49, 11433–11441 (2022). https://doi.org/10.1007/s11033-022-07677-7

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