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 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.

Download Full-text

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

Viruses ◽

10.3390/v13112230 ◽

2021 ◽

Vol 13 (11) ◽

pp. 2230

Author(s):

Roberto Ramos-Sobrinho ◽

Raphael O. Adegbola ◽

Kathy Lawrence ◽

Drew W. Schrimsher ◽

Thomas Isakeit ◽

...

Keyword(s):

South America ◽

Purifying Selection ◽

The United States ◽

Dwarf Virus ◽

Reading Frame ◽

Southern Us ◽

The Us ◽

Cotton Plants ◽

Variable Gene ◽

Cotton Leafroll Dwarf Virus

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.

Download Full-text

Cotton leafroll dwarf virus. [Distribution map].

Distribution Maps of Plant Diseases ◽

10.1079/dmpd/20203227932 ◽

2020 ◽

Author(s):

Keyword(s):

North Carolina ◽

South America ◽

Central African Republic ◽

East Timor ◽

Dwarf Virus ◽

Distribution Map ◽

Mato Grosso ◽

Virus Distribution ◽

New Distribution ◽

Cotton Leafroll Dwarf Virus

Abstract A new distribution map is provided for Cotton leafroll dwarf virus. Luteoviridae: Polerovirus. Hosts: cotton (Gossypium spp.), chickpea (Cicer arietinum). Information is given on the geographical distribution in Asia (East Timor, India, Maharashtra, Thailand, Uzbekistan), Africa (Central African Republic, Sudan), North America (USA, Alabama, Georgia, Mississippi, North Carolina, Texas), South America (Argentina, Brazil, Goias, Mato Grosso, Minas Gerais, Parana, Sao Paulo).

Download Full-text

P0 protein of cotton leafroll dwarf virus‐atypical isolate is a weak RNA silencing suppressor and the avirulence determinant that breaks the cotton Cbd gene‐based resistance

Plant Pathology ◽

10.1111/ppa.13031 ◽

2019 ◽

Vol 68 (6) ◽

pp. 1059-1071 ◽

Cited By ~ 1

Author(s):

Y. C. Agrofoglio ◽

V. C. Delfosse ◽

M. F. Casse ◽

H. E. Hopp ◽

I. Bonacic Kresic ◽

...

Keyword(s):

Rna Silencing ◽

Dwarf Virus ◽

Silencing Suppressor ◽

Rna Silencing Suppressor ◽

P0 Protein ◽

Cotton Leafroll Dwarf Virus

Download Full-text

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.734386 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ved Parkash ◽

Divya Bhanu Sharma ◽

John Snider ◽

Sudeep Bag ◽

Phillip Roberts ◽

...

Keyword(s):

United States ◽

Stomatal Conductance ◽

Gas Exchange ◽

Leaf Gas Exchange ◽

Genotypic Variation ◽

The United States ◽

Leaf Temperature ◽

Dwarf Virus ◽

Cotton Production ◽

Cotton Leafroll Dwarf Virus

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.

Download Full-text

Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

Virology Journal ◽

10.1186/s12985-020-01466-z ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Edith Khamonya Avedi ◽

Adedapo Olutola Adediji ◽

Dora Chao Kilalo ◽

Florence Mmogi Olubayo ◽

Isaac Macharia ◽

...

Keyword(s):

Genetic Diversity ◽

Selection Pressure ◽

Management Strategies ◽

Purifying Selection ◽

Tomato Leaf ◽

Amino Acid Sequences ◽

Virus Population ◽

Tomato Production ◽

Tomato Leaf Curl ◽

Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

Download Full-text

Molecular Analysis of a Plum pox virus W Isolate in Plum Germplasm Hand Carried into the USA from the Ukraine Shows a Close Relationship to a Latvian Isolate

Plant Disease ◽

10.1094/pdis-01-12-0104-re ◽

2013 ◽

Vol 97 (1) ◽

pp. 44-52 ◽

Cited By ~ 14

Author(s):

Vessela Mavrodieva ◽

Delano James ◽

Karen Williams ◽

Sarika Negi ◽

Aniko Varga ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

The United States ◽

Common Source ◽

Plum Pox Virus ◽

High Genetic Diversity ◽

Close Relationship ◽

The Usa ◽

Sequence Identities ◽

Germplasm Accessions

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

Download Full-text

High genetic diversity but low population structure in the frog Pseudopaludicola falcipes (Hensel, 1867) (Amphibia, Anura) from the Pampas of South America

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2015.11.012 ◽

2016 ◽

Vol 95 ◽

pp. 137-151 ◽

Cited By ~ 12

Author(s):

José A. Langone ◽

Arley Camargo ◽

Rafael O. de Sá

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

South America ◽

High Genetic Diversity

Download Full-text

The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia

Viruses ◽

10.3390/v10030136 ◽

2018 ◽

Vol 10 (3) ◽

pp. 136 ◽

Cited By ~ 4

Author(s):

Wycliff Kinoti ◽

Fiona Constable ◽

Narelle Nancarrow ◽

Kim Plummer ◽

Brendan Rodoni

Keyword(s):

Genetic Diversity ◽

Mosaic Virus ◽

Dwarf Virus ◽

Prunus Species ◽

Prune Dwarf Virus

Download Full-text

Reanalysis of Flash Floods and Debris Flows on two continents and their management strategies

10.5194/egusphere-egu21-373 ◽

2021 ◽

Author(s):

Juan Daniel Rios-Arboleda

Keyword(s):

Risk Management ◽

Developing Countries ◽

South America ◽

Debris Flow ◽

Debris Flows ◽

Large Scale ◽

Management Strategies ◽

Original Analysis ◽

Risk Management Strategies ◽

Latitudinal Patterns

This research expands the original analysis of Baker and Costa (1987) including data from Europe and South America with the objective to understand if there are emerging latitudinal patterns. In addition, the threshold proposed by Zimmermann et al. (1997) it is evaluated with the data from tropical zones finding that this is a good predictor.Mainly, recent Debris Flow occurred in South America are analyzed with the aim of identifying the best risk management strategies and their replicability for developing countries, particularly, the cases that have occurred in Colombia and Venezuela in the last 30 years are analyzed in order to compare management strategies and understand which are the most vulnerable areas to this phenomenon.It is concluded that large-scale and multinational projects such as SED ALP are required in South America to better characterize events that have left multiple fatalities (sometimes hundreds of people) and better understand how to manage the risk on densely populated areas.Finally, the use of amateur videos is proposed to characterize these events in nations with limited budgets for projects such as SED ALP, methodology that will be described extensively in later works.

Download Full-text