Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion

Wardatou Boukari, Ricardo I. Alcalá-Briseño, Simona Kraberger, Emmanuel Fernandez, Denis Filloux, Jean Heinrich Daugrois, Jack C. Comstock, Jean Michel Lett, Darren P. Martin, Arvind Varsani, Philippe Roumagnac, Jane E. Polston, Philippe C. Rott

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. Results: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion. Conclusions: As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

Original languageEnglish (US)
Article number146
JournalVirology Journal
Volume14
Issue number1
DOIs
StatePublished - Jul 28 2017

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Guadeloupe
Geminiviridae
Saccharum
Viruses
Genome
Barbados
West Indies
Metagenomics

Keywords

  • Geminiviridae
  • Mastrevirus
  • Saccharum spp.
  • Sugarcane
  • Sugarcane striate virus

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

Cite this

Boukari, W., Alcalá-Briseño, R. I., Kraberger, S., Fernandez, E., Filloux, D., Daugrois, J. H., ... Rott, P. C. (2017). Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion. Virology Journal, 14(1), [146]. https://doi.org/10.1186/s12985-017-0810-9

Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion. / Boukari, Wardatou; Alcalá-Briseño, Ricardo I.; Kraberger, Simona; Fernandez, Emmanuel; Filloux, Denis; Daugrois, Jean Heinrich; Comstock, Jack C.; Lett, Jean Michel; Martin, Darren P.; Varsani, Arvind; Roumagnac, Philippe; Polston, Jane E.; Rott, Philippe C.

In: Virology Journal, Vol. 14, No. 1, 146, 28.07.2017.

Research output: Contribution to journalArticle

Boukari, W, Alcalá-Briseño, RI, Kraberger, S, Fernandez, E, Filloux, D, Daugrois, JH, Comstock, JC, Lett, JM, Martin, DP, Varsani, A, Roumagnac, P, Polston, JE & Rott, PC 2017, 'Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion', Virology Journal, vol. 14, no. 1, 146. https://doi.org/10.1186/s12985-017-0810-9
Boukari W, Alcalá-Briseño RI, Kraberger S, Fernandez E, Filloux D, Daugrois JH et al. Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion. Virology Journal. 2017 Jul 28;14(1). 146. https://doi.org/10.1186/s12985-017-0810-9
Boukari, Wardatou ; Alcalá-Briseño, Ricardo I. ; Kraberger, Simona ; Fernandez, Emmanuel ; Filloux, Denis ; Daugrois, Jean Heinrich ; Comstock, Jack C. ; Lett, Jean Michel ; Martin, Darren P. ; Varsani, Arvind ; Roumagnac, Philippe ; Polston, Jane E. ; Rott, Philippe C. / Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion. In: Virology Journal. 2017 ; Vol. 14, No. 1.
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abstract = "Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and R{\'e}union (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. Results: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88{\%} genome-wide pairwise identity with one another and between 89 and 97{\%} identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in R{\'e}union. Conclusions: As these virus isolates share <64{\%} genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.",
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AU - Boukari, Wardatou

AU - Alcalá-Briseño, Ricardo I.

AU - Kraberger, Simona

AU - Fernandez, Emmanuel

AU - Filloux, Denis

AU - Daugrois, Jean Heinrich

AU - Comstock, Jack C.

AU - Lett, Jean Michel

AU - Martin, Darren P.

AU - Varsani, Arvind

AU - Roumagnac, Philippe

AU - Polston, Jane E.

AU - Rott, Philippe C.

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N2 - Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. Results: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion. Conclusions: As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

AB - Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. Results: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion. Conclusions: As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

KW - Geminiviridae

KW - Mastrevirus

KW - Saccharum spp.

KW - Sugarcane

KW - Sugarcane striate virus

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