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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Authors: | Shuo Cheng Zhang Kai-Shu Ling |
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Institution: | (1) Center for Biotechnology and Genomics, Alcorn State University, Alcorn State, MS 39096, USA;(2) Present address: Institute for Nutrisciences and Health, National Research Council Canada, Charlottetown, PE, C1A 5T1, Canada;(3) U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research Service, 2700 Savannah Highway, Charleston, SC 29414, USA; |
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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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