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Genetic diversity of sweet potato begomoviruses in the United States and identification of a natural recombinant between sweet potato leaf curl virus and sweet potato leaf curl Georgia virus

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Abstract

In the United States, two sweet potato begomoviruses, sweet potato leaf curl virus (SPLCV) and sweet potato leaf curl Georgia virus (SPLCGV), were previously identified in Louisiana. In recent years, at least seven additional sweet potato begomoviruses have been identified in other parts of the world. In an effort to determine the genetic diversity and distribution of sweet potato begomoviruses in the U.S., we focused our efforts on molecular characterization of field-collected begomovirus isolates in two states: Mississippi and South Carolina. Using rolling-circle amplification, a total of 52 clones of the full genome were obtained. Initial inspection of alignments of the end sequences in these clones revealed a strong genetic diversity. Overall, 10 genotypes could be assigned. A majority of the isolates (50/52) in eight genotypes were shown to be closely related to SPLCV. A representative clone of each genotype was fully sequenced and analyzed. Among them, four genotypes from South Carolina with 91-92% sequence identity to the type member of SPLCV were considered a new strain, whereas four other genotypes from Mississippi with >95% sequence identity to SPLCV were considered variants. In addition, a member of a proposed new begomovirus species was identified after comparative sequence analysis of the isolate [US:SC:646B-9] from South Carolina with less than 89% sequence identity to any known begomovirus. Hence, the provisional name Sweet potato leaf curl South Carolina virus (SPLCSCV) is proposed. Moreover, a natural recombinant consisting of two distinct parental genomic sequences from SPLCV and SPLCGV was identified in the sample [US:MS:1B-3] from Mississippi. Two recombinant breakpoints were identified, one in the origin of replication and the other between C2 and C4. This knowledge about the genetic diversity of begomoviruses infecting sweet potato will likely have a major impact on PCR-based virus detection and on disease management practice through breeding for virus resistance.

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Acknowledgments

We thank Dr. D. Michael Jackson and Alvin Simmons for critical reading of the manuscript, and Andrea Gilliard and Kim Bowie for excellent technical assistance. Funding for this research was supported in part by a USDA-NIFA grant.

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  1. Shuo Cheng Zhang

    Present address: Institute for Nutrisciences and Health, National Research Council Canada, Charlottetown, PE, C1A 5T1, Canada

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  1. Center for Biotechnology and Genomics, Alcorn State University, Alcorn State, MS, 39096, USA

    Shuo Cheng Zhang

  2. U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research Service, 2700 Savannah Highway, Charleston, SC, 29414, USA

    Kai-Shu Ling

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Zhang, S.C., Ling, KS. Genetic diversity of sweet potato begomoviruses in the United States and identification of a natural recombinant between sweet potato leaf curl virus and sweet potato leaf curl Georgia virus. Arch Virol 156, 955–968 (2011). https://doi.org/10.1007/s00705-011-0930-2

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