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

Tabassum, Afsha; Bag, Sudeep; Suassuna, N. D.; Conner, Kassie; Chee, Peng W.; Kemerait, Robert C.; Roberts, Phillip M.

doi:10.1371/journal.pone.0252523

Cited by 11 publications

(20 citation statements)

References 41 publications

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“…CLRDV was also detected from a high percentage of asymptomatic plants of all other cultivars assessed (data not shown; DG3615, ST 5600 B2XF and DP 1851 B3XF in 2019 and ST 5122 GLT in 2020). The near-complete sequence of the CLRDV genome was generated from these symptomatic plant tissues and submitted to NCBI GenBank (MT800932) as part of a concurrent research effort (Tabassum et al, 2021).…”

Section: Virus Detectionmentioning

confidence: 99%

“…Numerous symptoms have been associated with CLRDD. A few of the notable symptoms include reddening of leaves and petioles, leaf wilting, subsequent drooping, crinkling, and deformation of the leaves above the nodes, which had reddened leaves, development of intense green foliage, and shortening of upper internodes resulting in stunted plants (Tabassum et al, 2019(Tabassum et al, , 2020Bag et al, 2021). Severe disease infection could result in reduced boll set and lower seed-cotton yield per plant (Avelar et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…CLRDV is a positive sense, single-stranded RNA virus, and it is a phloem-limited virus, meaning it replicates and circulates mainly in the phloem tissue of the host plant (Silva et al, 2008;Jiménez et al, 2021). In the United States, the partial genome sequence of CLRDV was first sequenced from isolates collected from Alabama (Avelar et al, 2020), and the complete genome was subsequently completed from an isolate collected in Georgia (Tabassum et al, 2020(Tabassum et al, , 2021. The genomic sequence of the CLRDV isolate from Georgia was between 95 and 98% identical to the genome of other CLRDV isolates reported in the United States (Alabama, GenBank accession number MN071395; Texas, MN872302) and South America (KF359947, KF906261, KF906260, NC_014545, GU167940, and HQ827780; Tabassum et al, 2020Tabassum et al, , 2021.…”

Section: Introductionmentioning

confidence: 99%

“…In the United States, the partial genome sequence of CLRDV was first sequenced from isolates collected from Alabama (Avelar et al, 2020), and the complete genome was subsequently completed from an isolate collected in Georgia (Tabassum et al, 2020(Tabassum et al, , 2021. The genomic sequence of the CLRDV isolate from Georgia was between 95 and 98% identical to the genome of other CLRDV isolates reported in the United States (Alabama, GenBank accession number MN071395; Texas, MN872302) and South America (KF359947, KF906261, KF906260, NC_014545, GU167940, and HQ827780; Tabassum et al, 2020Tabassum et al, , 2021. Despite obvious genomic similarity, there are three unique genotypes of CLRDV recognized globally: "atypical, " "typical, " and "CLRDV-US" (Avelar et al, 2020;Iriarte et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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Effect of Cotton Leafroll Dwarf Virus on Physiological Processes and Yield of Individual Cotton Plants

et al. 2021

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Cotton leafroll dwarf disease (CLRDD) caused by cotton leafroll dwarf virus (CLRDV) is an emerging threat to cotton production in the United States. The disease was first reported in Alabama in 2017 and subsequently has been reported in 10 other cotton producing states in the United States, including Georgia. A field study was conducted at field sites near Tifton, Georgia in 2019 and 2020 to evaluate leaf gas exchange, chlorophyll fluorescence, and leaf temperature responses for a symptomatic cultivar (diseased plants observed at regular frequency) at multiple stages of disease progression and for asymptomatic cultivars (0% disease incidence observed). Disease-induced reductions in net photosynthetic rate (An, decreased by 63–101%), stomatal conductance (gs, decreased by 65–99%), and efficiency of the thylakoid reactions (32–92% decline in primary photochemistry) were observed, whereas leaf temperature significantly increased by 0.5–3.8°C at advanced stages of the disease. Net photosynthesis was substantially more sensitive to disease-induced declines in gs than the thylakoid reactions. Symptomatic plants with more advanced disease stages remained stunted throughout the growing season, and yield was reduced by 99% by CLRDD due to reductions in boll number per plant and declines in boll mass resulting from fewer seeds per boll. Asymptomatic cultivars exhibited more conservative gas exchange responses than apparently healthy plants of the symptomatic cultivar but were less productive. Overall, it is concluded that CLRDV limits stomatal conductance and photosynthetic activity of individual leaves, causing substantial declines in productivity for individual plants. Future studies should evaluate the physiological contributors to genotypic variation in disease tolerance under controlled conditions.

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Section: Virus Detectionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Effect of Cotton Leafroll Dwarf Virus on Physiological Processes and Yield of Individual Cotton Plants

et al. 2021

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“…The P0 silencing suppressor, encoded by the CLRDV ORF0, is the most variable coding region at both nucleotide and amino acid levels [32,40,[57][58][59]. Despite the recent increased spread and emergence of CLRD disease and its detrimental effects on cotton productivity worldwide, there is little understanding of the genetic structure of CLRDV populations.…”

Section: Introductionmentioning

confidence: 99%

Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability

Ramos-Sobrinho

Adegbola

Lawrence

et al. 2021

Viruses

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Cotton leafroll dwarf virus (CLRDV) was first reported in the United States (US) in 2017 from cotton plants in Alabama (AL) and has become widespread in cotton-growing states of the southern US. To investigate the genomic variability among CLRDV isolates in the US, complete genomes of the virus were obtained from infected cotton plants displaying mild to severe symptoms from AL, Florida, and Texas. Eight CLRDV genomes were determined, ranging in size from 5865 to 5867 bp, and shared highest nucleotide identity with other CLRDV isolates in the US, at 95.9–98.7%. Open reading frame (ORF) 0, encoding the P0 silencing suppressor, was the most variable gene, sharing 88.5–99.6% and 81.2–89.3% amino acid similarity with CLRDV isolates reported in cotton growing states in the US and in Argentina and Brazil in South America, respectively. Based on Bayesian analysis, the complete CLRDV genomes from cotton in the US formed a monophyletic group comprising three relatively divergent sister clades, whereas CLRDV genotypes from South America clustered as closely related sister-groups, separate from US isolates, patterns reminiscent of phylogeographical structuring. The CLRDV isolates exhibited a complex pattern of recombination, with most breakpoints evident in ORFs 2 and 3, and ORF5. Despite extensive nucleotide diversity among all available CLRDV genomes, purifying selection (dN/dS < 1) was implicated as the primary selective force acting on viral protein evolution.

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Characterizing the vector competence of Aphis gossypii, Myzus persicae and Aphis craccivora (Hemiptera: Aphididae) to transmit cotton leafroll dwarf virus to cotton in the United States

Heilsnis,

Mahas,

Conner

et al. 2023

Journal of Economic Entomology

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Cotton leafroll dwarf virus (CLRDV) is a yield-limiting, aphid-transmitted virus that was identified in cotton, Gossypium hirsutum L., in the United States of America in 2017. CLRDV is currently classified in the genus Polerovirus, family Solemoviridae. Although 8 species of aphids (Hemiptera: Aphididae) are reported to infest cotton, Aphis gossypii Glover is the only known vector of CLRDV to this crop. Aphis gossypii transmits CLRDV in a persistent and nonpropagative manner, but acquisition and retention times have only been partially characterized in Brazil. The main objectives of this study were to characterize the acquisition access period, the inoculation access period, and retention times for a U.S. strain of CLRDV and A. gossypii population. A sub-objective was to test the vector competence of Myzus persicae Sulzer and Aphis craccivora Koch. In our study, A. gossypii apterous and alate morphs were able to acquire CLRDV in 30 min and 24 h, inoculate CLRDV in 45 and 15 min, and retain CLRDV for 15 and 23 days, respectively. Neither M. persicae nor A. craccivora acquired or transmitted CLRDV to cotton.

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

Cited by 11 publications

References 41 publications

Effect of Cotton Leafroll Dwarf Virus on Physiological Processes and Yield of Individual Cotton Plants

Effect of Cotton Leafroll Dwarf Virus on Physiological Processes and Yield of Individual Cotton Plants

Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability

Characterizing the vector competence of Aphis gossypii, Myzus persicae and Aphis craccivora (Hemiptera: Aphididae) to transmit cotton leafroll dwarf virus to cotton in the United States

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