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Journal of Plant Biochemistry and Biotechnology

, Volume 27, Issue 4, pp 382–392 | Cite as

Comparative characterization of small RNAs derived from an emaravirus and a geminivirus infecting pigeonpea

  • Basavaprabhu L. Patil
  • Deepika Arora
Original Article
  • 138 Downloads

Abstract

High throughput sequencing technologies, supported by bioinformatics tools are employed to retrieve small RNA sequence information derived from the nucleic acids of plant infecting viruses. In addition to characterization of the small RNAs to understand the biology of the virus, the small RNA sequence can be assembled to reconstitute viral genome sequence. For the first time the semiconductor based Ion Proton sequencing technology is used to sequence the small RNAs from pigeonpea (Cajanus cajan) plants infected by two distinct viruses with RNA and DNA as their genomes. The reconstitution of the viral genome sequence revealed that the pigeonpea plant from Kalaburagi (erstwhile Gulbarga, Karnataka state) was infected by an emaravirus species Pigeonpea sterility mosaic emaravirus 1 (PPSMV-1) and another plant from New Delhi was infected by a begomovirus species Mungbean yellow mosaic India virus (MYMIV). Characterization and comparison of small RNA sequences derived from both the viruses showed vast differences in their pattern of accumulation and their size classes. In the case of PPSMV-1, the 21 nt sized siRNAs accumulated at far greater levels followed by 22 and 24 nt siRNAs. Whereas in MYMIV, the proportion of accumulation of each size class of siRNAs was similar. Further the distribution of small RNAs across the genomes of PPSMV-1 and MYMIV was mapped and the density of small RNA accumulation showed a positive correlation with the GC content of viral sequence.

Keywords

Emaravirus Geminivirus Pigeonpea Small RNA Next generation sequencing Ion Proton 

Notes

Acknowledgements

BLP acknowledges the research funding and DA acknowledges the young professional fellowship from ICAR-NRCPB. We thank Mr. Pravin Nilawe from Thermo Fisher Scientific for his help in bioinformatics analysis.

Author contributions

BLP designed and carried out all the experiments and wrote the manuscript. DA helped in validation of PPSMV-1 sequence by RT-PCR.

Compliance with ethical standards

Conflict of interest

Both authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

13562_2018_447_MOESM1_ESM.docx (20 kb)
Supplementary material 1 (DOCX 19 kb)

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Copyright information

© Society for Plant Biochemistry and Biotechnology 2018

Authors and Affiliations

  1. 1.ICAR-National Research Centre on Plant BiotechnologyNew DelhiIndia

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