Genome analysis of cotton leafroll dwarf virus reveals variability in the silencing suppressor protein, genotypes and genomic recombinants in the USA

Cotton leafroll dwarf virus (CLRDV) is an emerging virus in cotton production in Georgia and several other Southeastern states in the USA. To better understand the genetic diversity of the virus population, the near complete genome sequences of six isolates from Georgia and one from Alabama were det...

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Bibliographic Details
Published in:PloS one 2021-07, Vol.16 (7), p.e0252523
Main Authors: Tabassum, Afsha, Bag, Sudeep, Suassuna, Nelson D, Conner, Kassie N, Chee, Peng, Kemerait, Robert C, Roberts, Phillip
Format: Article
Language:English
Subjects:
Amino acids
Analysis
Biology and Life Sciences
Computer and Information Sciences
Cotton
Data collection
Flowers & plants
Gene sequencing
Genetic diversity
Genetic Variation
Genome, Viral
Genomes
Genotype
Genotypes
Georgia
Gossypium - genetics
Gossypium - virology
Isoleucine
Luteoviridae - classification
Luteoviridae - genetics
Luteoviridae - isolation & purification
Nucleotides
Open reading frames
Open Reading Frames - genetics
People and places
Phylogeny
Plant Diseases - virology
Plant pathology
Population
Population genetics
Population structure
Proteins
Recombinants
Recombination, Genetic
Research and Analysis Methods
United States
Valine
Viral Proteins - genetics
Viruses
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Summary:Cotton leafroll dwarf virus (CLRDV) is an emerging virus in cotton production in Georgia and several other Southeastern states in the USA. To better understand the genetic diversity of the virus population, the near complete genome sequences of six isolates from Georgia and one from Alabama were determined. The isolates sequenced were 5,866 nucleotides with seven open reading frames (ORFs). The isolates from Georgia were >94% identical with other isolates from the USA and South America. In the silencing suppressor protein (P0), at amino acid position 72, the isolates from Georgia and Alabama had a valine (V), similar to resistant-breaking 'atypical' genotypes in South America, while the Texas isolate had isoleucine (I), similar to the more aggressive 'typical' genotypes of CLRDV. At position 120, arginine (R) is unique to Georgia and China isolates, but absent in Alabama, Texas and South American isolates. Ten potential recombinant events were detected in the isolates sequenced. An increased understanding of CLRDV population structure and genetic diversity will help develop management strategies for CLRDV in the USA cotton belt.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0252523