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ARS Home » Northeast Area » Washington, D.C. » National Arboretum » Floral and Nursery Plants Research » Research » Publications at this Location » Publication #312819
Title: Leek yellow stripe virus isolates from Brazil form a distant clade based on the P1 gene

Author
item BAMPI, DAIANA - Universidade Estadual Jullo De Mesqulta Filho
item MITUTI, TATIANA - Luiz De Queiroz College Of Agriculture (ESALQ)
item PAVEN, MARCELO - Universidade Estadual Jullo De Mesqulta Filho
item Hammond, John
item KRAUSE-SAKATE, RENATE - Universidade Estadual Jullo De Mesqulta Filho

Submitted to: Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/13/2015
Publication Date: 12/15/2015
Citation: Bampi, D., Mituti, T., Paven, M.A., Hammond, J., Krause-Sakate, R. 2015. Leek yellow stripe virus isolates from Brazil form a distant clade based on the P1 gene. Journal of Plant Pathology. 97:457-463.

Interpretive Summary: The edible Allium crops of garlic, onion, and leek are grown almost worldwide, and are commonly infected by multiple viruses that reduce both yield and quality. Garlic is produced by vegetative propagation, and all of the viruses are transmitted both through vegetative propagation and by insect or mite vectors. The viruses therefore easily re-infect virus-free garlic when it is planted in the field, so efficient virus detection and rapid removal of infected plants is essential to maintain crop health. Different isolates of the viruses are prevalent in various parts of the world, and vary in the severity of disease; the P1 protein of Leek yellow stripe virus (LYSV) differs in both length and sequence between isolates, and is thought to contribute to disease severity. S-type isolates of LYSV have a significant deletion in the P1 gene compared to N-type isolates, and have different geographical distribution around the world. The complete sequence of one LYSV isolate from Brazil was therefore determined, together with the sequence of a portion of the P1 gene of multiple other LYSV isolates from different regions of Brazil, in order to examine divergence. All Brazilian LYSV isolates were found to be most similar to each other, and most closely related to an isolate from Okinawa, Japan, and to be phylogenetically most similar to S-type isolates except that all lack the P1 deletion present in S-type isolates. This suggests that the Brazilian isolates are derived from an ancestral source of the S-type isolates, prior to the occurrence of the deletion in the P1 gene and subsequent divergence of S-type isolates. This information will aid in selection and maintenance of virus-free garlic and further research into differences in disease severity between LYSV isolates, for the benefit of garlic breeders and producers.

Technical Abstract: The complete genomic sequence of a garlic isolate of Leek yellow stripe virus from Brazil (LYSV-MG) has been determined, and phylogenetic comparisons made to LYSV isolates from other parts of the world. In addition, the nucleotide sequence of the 5'UTR and part of the P1 gene of multiple LYSV isolates collected from several locations in Brazil were determined and used to refine their phylogenetic relationships. The LYSV-MG genome consists of 10,341 nucleotides and encodes a deduced polyprotein of 3,221 amino acids. LYSV isolates are separated into two main groups (N-type and S-type); S-type viruses have a large deletion in the P1 gene compared to N-type viruses. Brazilian isolates do not have this deletion, but are more closely related to S-type than to N-type isolates. Brazilian isolates share 97-99% of 5'UTR-P1 region nucleotide identity with each other, and 51-64% with different isolates from around the world. The Brazilian isolates formed a monophyletic group closer to one isolate from Okinawa. The data suggest that Brazilian LYSV isolates are derived from an ancestral source of the Okinawa and S-type isolates, prior to the occurrence of the P1 deletion and divergence in the S-type isolates.