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

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...

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Autores principales:	Roberto Ramos-Sobrinho, Raphael O. Adegbola, Kathy Lawrence, Drew W. Schrimsher, Thomas Isakeit, Olufemi J. Alabi, Judith K. Brown
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	cotton viruses genetic diversity plant virus evolution <i>Polerovirus</i> <i>Solemoviridae</i> Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1e70edd8ffc745aeae0c58ef1ee620ab
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spelling	oai:doaj.org-article:1e70edd8ffc745aeae0c58ef1ee620ab2021-11-25T19:13:34ZCotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability10.3390/v131122301999-4915https://doaj.org/article/1e70edd8ffc745aeae0c58ef1ee620ab2021-11-01T00:00:00Zhttps://www.mdpi.com/1999-4915/13/11/2230https://doaj.org/toc/1999-4915Cotton 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 (<i>dN/dS</i> < 1) was implicated as the primary selective force acting on viral protein evolution.Roberto Ramos-SobrinhoRaphael O. AdegbolaKathy LawrenceDrew W. SchrimsherThomas IsakeitOlufemi J. AlabiJudith K. BrownMDPI AGarticlecotton virusesgenetic diversityplant virus evolution<i>Polerovirus</i><i>Solemoviridae</i>MicrobiologyQR1-502ENViruses, Vol 13, Iss 2230, p 2230 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	cotton viruses genetic diversity plant virus evolution <i>Polerovirus</i> <i>Solemoviridae</i> Microbiology QR1-502
spellingShingle	cotton viruses genetic diversity plant virus evolution <i>Polerovirus</i> <i>Solemoviridae</i> Microbiology QR1-502 Roberto Ramos-Sobrinho Raphael O. Adegbola Kathy Lawrence Drew W. Schrimsher Thomas Isakeit Olufemi J. Alabi Judith K. Brown Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability
description	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 (<i>dN/dS</i> < 1) was implicated as the primary selective force acting on viral protein evolution.
format	article
author	Roberto Ramos-Sobrinho Raphael O. Adegbola Kathy Lawrence Drew W. Schrimsher Thomas Isakeit Olufemi J. Alabi Judith K. Brown
author_facet	Roberto Ramos-Sobrinho Raphael O. Adegbola Kathy Lawrence Drew W. Schrimsher Thomas Isakeit Olufemi J. Alabi Judith K. Brown
author_sort	Roberto Ramos-Sobrinho
title	Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability
title_short	Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability
title_full	Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability
title_fullStr	Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability
title_full_unstemmed	Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability
title_sort	cotton leafroll dwarf virus us genomes comprise divergent subpopulations and harbor extensive variability
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/1e70edd8ffc745aeae0c58ef1ee620ab
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Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability

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