Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Reunion
2017
Boukari, Wardatou | Alcala-Briseno, Ricardo I. | Kraberger, Simona | Fernandez, Emmanuel | Filloux, Denis | Daugrois, Jean-Heindrich | Comstock, Jack C. | Lett, Jean-Michel | Martin, Darren P. | Varsani, Arvind | Roumagnac, Philippe | Polston, Jane E. | Rott, Philippe C. | IFAS, Everglades Research & Education Center ; University of Florida [Gainesville] (UF) | IFAS, Plant pathology Department ; University of Florida [Gainesville] (UF) | The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences ; Arizona State University [Tempe] (ASU) | Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) | Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) | Institut National de la Recherche Agronomique (INRA) | Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) | Sugarcane Field Station ; USDA-ARS : Agricultural Research Service | Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR) | Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, Observatory ; University of Cape Town | Structural Biology Research Unit, Department of Clinical Laboratory Sciences ; University of Cape Town | Florida Sugar Cane League : 00107475, F000057 ; USDA National Institute of Food and Agriculture : Hatch/Rott FLA-BGL-005404 ; Region Reunion ; European Union (FEDER) : 1.03 ; National Research Foundation of South Africa ; EU grant FP7-PEOPLE-IOF : PIOF-GA-2013-622571
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 Reunion (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 Reunion. 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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