The Complete Nucleotide Sequence of a Korean Isolate Bean yellow mosaic virus from Freesia sp. and Comparison to Other Potyviruses

Research in Plant Disease 2013;19(2):77-83.
Published online June 30, 2013.

Sun-Hee Choi1†, Ju-Yeon Yoon1†, Ki-Hyun Ryu1 and Seung-Kook Choi2*

¹Department of Horticulture and Landscape, College of Natural Science, Seoul Women’s University, Seoul 139-774, Korea
²Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 441-440, Korea

Received: April 01, 2013 Revised: April 22, 2013 Accepted: May 02, 2013

Abstract

Bean yellow mosaic virus (BYMV; genus Potyvirus, family Potyviridae) causes severe losses to various legume species and a number of non-legume species, particularly freesia plants. In a survey of virus diseases in Gyeonggi province, Korea, BYMV isolates were identified from many cultivated freesia species. Here, we determined the complete nucleotide sequences of a BYMV freesia isolate (BYMV-Fr; accession number FJ492961). BYMV-Fr genome consists of 9,545 nucleotides (nt) excluding the poly (A) tail and encodes 3,057 amino acid (aa), with an AUG start and UAG stop codon, containing one open reading frame typical of a potyvirus polyprotein. The polyprotein of BYMV-Fr was divided to ten proteins and the cleavage sites of each protein were determined. The coat protein (CP) and polyprotein of BYMV-Fr were compared at the aa level with those of the previously reported 4 BYMV isolates. BYMV-Fr shared 90.1 to 97.1 and 91.0 to 92.5% at the CP and polyprotein homology. Interestingly, BYMV-Fr showed identities of a lower level at the nt level of 5' noncoding region (61.4 to 67.6%) and at the aa level of P1 (71.4 to 72.8%), comparing with four BYMV isolates. Based on the aa sequence diversity of CP and polyprotein, phylogenetic analysis with the four BYMV isolates showed two distinct groups and BYMV-Fr and most BYMV isolates were most closely related to the clover yellow vein virus among 52 potyviruses. To our knowledge, this is the first report of the complete genome sequence of BYMV freesia strain.

Key Words: Bean yellow mosaic virus, Freesia, Genetic diversity, Potyvirus, RT-PCR, Sequence analysis