Articles
MOLECULAR CLONING AND NUCLEOTIDE SEQUENCE ANALYSIS OF THE S RNA OF WATERMELON SILVER MOTTLE VIRUS
Article number
431_22
Pages
244 – 260
Language
Abstract
The nucleotide (nt) sequence of the nucleocapsid (N) gene of watermelon silver mottle virus (WSMV) was previously and found to be distinct from four other tospoviruses.
In this study, dsRNA of WSMV was extracted from virus-infected Chenopodium quinoa and used for cDNA cloning by random priming.
The 5′-and 3′-terminal sequences were determined by polymerase chain reaction (PCR) amplification and cloning.
The complete nt sequence of the S RNA of WSMV contained 3,534 nt.
The open-reading frame (ORF) of the nonstructural protein (NSs) located on the viral strand of S RNA contained 1,317 nt, coding for a protein of 439 amino acids.
Comparison of the nt sequence of the WSMV NSs gene with those of three isolates of tospoviruses (TSWV-CPNH1, TSWV-L3, and INSV) revealed that their degrees of identity were 51.9–54.3%. The degrees of amino-acid identity were only 12.1–13.7%. The nt sequence of the intergenic region was A-U rich and 1,261 nt in length, 752 and 613 nt longer than those of TSWV-CPNH1 and INSV, respectively, and shared only 33.5% identity to that of TSWV-CPNH1 and 40.4% identity to INSV. The 5′ non-coding region of WSMV S RNA was 66 nt long, and shared 68.2% identity to that of TSWV. The 5′ and 3′-terminal sequences of the viral sense S RNA of WSMV were highly complementary over a stretch of 40 nt.
The first 14 nt at the 5′ end were perfectly paired with the last 14 nt at the 3′ end.
Comparison of S RNAs of WSMV, TSWV-CPNH1, and INSV revealed a consensus sequence of 8 nt of 5′-AGAGCAAU.…-3′ at their 5′ ends and 5′-.…AUUGCUCU-3′ at their 3′ ends.
These results strengthened the argument that WSMV belongs to the genus Tospovirus, but is distinct from known members.
Moreover, the overall nt identity of S RNA compared with that of a tomato tospovirus (Tospo-To), which also originated from Taiwan and belonged to serogroup IV, was 98.7%, indicating that Tospo-To is a strain of WSMV.
In this study, dsRNA of WSMV was extracted from virus-infected Chenopodium quinoa and used for cDNA cloning by random priming.
The 5′-and 3′-terminal sequences were determined by polymerase chain reaction (PCR) amplification and cloning.
The complete nt sequence of the S RNA of WSMV contained 3,534 nt.
The open-reading frame (ORF) of the nonstructural protein (NSs) located on the viral strand of S RNA contained 1,317 nt, coding for a protein of 439 amino acids.
Comparison of the nt sequence of the WSMV NSs gene with those of three isolates of tospoviruses (TSWV-CPNH1, TSWV-L3, and INSV) revealed that their degrees of identity were 51.9–54.3%. The degrees of amino-acid identity were only 12.1–13.7%. The nt sequence of the intergenic region was A-U rich and 1,261 nt in length, 752 and 613 nt longer than those of TSWV-CPNH1 and INSV, respectively, and shared only 33.5% identity to that of TSWV-CPNH1 and 40.4% identity to INSV. The 5′ non-coding region of WSMV S RNA was 66 nt long, and shared 68.2% identity to that of TSWV. The 5′ and 3′-terminal sequences of the viral sense S RNA of WSMV were highly complementary over a stretch of 40 nt.
The first 14 nt at the 5′ end were perfectly paired with the last 14 nt at the 3′ end.
Comparison of S RNAs of WSMV, TSWV-CPNH1, and INSV revealed a consensus sequence of 8 nt of 5′-AGAGCAAU.…-3′ at their 5′ ends and 5′-.…AUUGCUCU-3′ at their 3′ ends.
These results strengthened the argument that WSMV belongs to the genus Tospovirus, but is distinct from known members.
Moreover, the overall nt identity of S RNA compared with that of a tomato tospovirus (Tospo-To), which also originated from Taiwan and belonged to serogroup IV, was 98.7%, indicating that Tospo-To is a strain of WSMV.
Authors
S. Yeh, I. Sun, H. Ho, T. Chang
Keywords
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