Subpopulation level variation of banana streak viruses in India and common evolution of banana and sugarcane badnaviruses

Abstract

Genome sequences of three episomal Banana streak MY virus (BSMYV) isolates sampled from triploid banana hybrids (Chini Champa: AAB; Malbhog: AAB and Monthan: ABB), grown in North-East and South India are reported in this study by sequence-independent improved rolling circle amplification (RCA). RCA coupled with restriction fragment length polymorphism revealed diverse restriction profiles of five BSMYV isolates. Nucleotide substitution rates of BSMYV subpopulation and Banana streak OL virus subpopulation was 7.13 × 10−3 to 1.59 × 10−2 and 2.65 × 10−3 to 5.49 × 10−3, respectively, for the different coding regions. Analysis of the genetic diversity of banana and sugarcane badnaviruses revealed a total of 32 unique recombination events among banana and sugarcane badnaviruses (inter BSV–SCBV), in addition to the extensive recombination with in banana streak viruses and sugarcane bacilliform viruses (intra-BSV and intra-SCBV). Many unique fragments were shown to contain similar ruminant sequence fragments which indicated the possibility that the two groups of badnaviruses or their ancestors to colonise same host before making the host shift. The distribution of recombination events, hot-spots (intergenic region and C-terminal of ORF3) as well as cold-spots (distributed in ORF3) displayed the mirroring of recombination traces in both group of badnaviruses. These results support the hypothesis of relatedness of banana and sugarcane badnaviruses and the host and geographical shifts that followed the fixation of the species complex appear to be a recent event.

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Acknowledgments

The funding from ICAR Outreach Project is gratefully acknowledged. Authors are thankful to Head Division of Plant Pathology and Director ICAR-Indian Agricultural Research Institute for necessary lab facilities. First author is grateful to Department of Science and Technology for INSPIRE fellowship during PhD Programme. Authors are thankful to Dr. Siddarame Gowda and the anonymous reviewers for their comments and suggestions in improvement of manuscript.

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Correspondence to Virendra Kumar Baranwal.

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Edited by Karel Petrzik.

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Sharma, S.K., Vignesh Kumar, P., Geetanjali, A.S. et al. Subpopulation level variation of banana streak viruses in India and common evolution of banana and sugarcane badnaviruses. Virus Genes 50, 450–465 (2015). https://doi.org/10.1007/s11262-015-1179-8

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Keywords

  • Banana
  • Sugarcane
  • Badnaviruses
  • Host shift
  • Phylogeny
  • Recombination
  • Evolution