Completion of the genome sequence of Watermelon silver mottle virus and utilization of degenerate primers for detecting tospoviruses in five serogroups

• Published in: Phytopathology Vol. 91; no. 4; pp. 361 - 368
• Main Authors: CHU, Fang-Hua, CHAO, Chia-Hung, CHUNG, Min-Hsun, CHEN, Ching-Chung, YEH, Shyi-Dong
• Format: Journal Article
• Language: English
• Published: St. Paul, MN American Phytopathological Society 01.04.2001
• Subjects: Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Generalities. Techniques. Transmission, epidemiology, ecology. Antiviral substances, control; Phytopathology. Animal pests. Plant and forest protection; Plant viruses and viroids; Plant pathogen; Nucleotide sequence; Tospovirus; Serogroup; Primer; Homology; Identification; Phylogeny; Virus; Polymerase chain reaction; Bunyaviridae; RT-PCR; Detection; Aminoacid sequence
• ISSN: 0031-949X; 1943-7684
• DOI: 10.1094/PHYTO.2001.91.4.361

ABSTRACT The nucleotide sequence of the L RNA of Watermelon silver mottle virus (WSMoV) was determined. Combined with the previous work on M and S RNAs, the whole genomic sequence of this member of the genus Tospovirus was completed. The L RNA is 8,917 nucleotides in length, with one large open reading frame encoding a translation product of 2,878 amino acids (331.8 kDa) on the viral complementary strand. The L protein shares amino acid identities of only 44.3 and 46.5% with Tomato spotted wilt virus (TSWV) and Impatiens necrotic spot virus, respectively; but an amino acid identity of 91.3% with Peanut bud necrosis virus. Among the sequenced tospoviruses, L protein was the most conserved gene product, whereas the nonstructural S protein was generally the most variable. Comparison of the deduced L protein of WSMoV with those of other members of the family Bunyaviridae revealed that its amino acid sequence includes the reported conserved motifs of RNA-dependent RNA polymerases. To develop a method for detecting tospo-viruses by reverse transcription-polymerase chain reaction (RT-PCR), two pairs of degenerate primers were designed from conserved regions of the L genes and used to amplify the corresponding regions of the L genes from total RNAs extracted from plant tissues infected with five serologically distinct tospoviruses. The DNA fragments obtained were identified as those of tospoviruses by restriction enzyme digestion and DNA sequencing. For field samples, watermelon and wax gourd infected with WSMoV, and lisianthus infected with TSWV were also successfully detected by these two pairs of degenerate primers, with a sensitivity similar to N-gene-specific primers. The results indicated that the RT-PCR with the degenerate primers is a fast and reliable method for detecting tospoviruses in different serogroups.