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United States Department of Agriculture

Agricultural Research Service

Title: Non-Uniform Pattern of Sequence Divergence Between Oat Necrotic Mottle Virus and Wheat Streak Mosaic Virus

Authors
item French, Roy
item Rabenstein, Frank - IRRPD, GERMANY
item Seifers, Dallas - KS STATE UNIVERSITY
item Schubert, Jorg - IRRPD, GERMANY
item Stenger, Drake

Submitted to: American Society for Virology Meeting
Publication Type: Abstract Only
Publication Acceptance Date: May 1, 2002
Publication Date: July 25, 2002
Citation: French, R.C., Rabenstein, F., Seifers, D.L., Schubert, J., Stenger, D.C. 2002. Non-uniform pattern of sequence divergence between oat necrotic mottle virus and wheat streak mosaic virus. American Society For Virology Meeting. Not published by meeting.

Technical Abstract: The sequence of the 3'-terminal 1729 nucleotides (nts) of two ONMV isolates were determined and compared with sequences of WSMV isolates Czech Republic, Hungary, Iran, Mexico, Russia, Turkey and the U.S.A. The WSMV sequences shared 73-74% (nt) and 79¿81% (amino acid [aa]) identity with ONMV. In contrast, ONMV is only 37% (nt) and 24% (aa) identical to RGMV. Thus, ONMV should be removed from the genus Rymovirus (where it appears in the 7th report of the ICTV) and placed in the genus Tritimovirus. The coat protein (CP) cistron of ONMV was 12 codons shorter than the WSMV consensus sequence. However, sequence identities were sufficiently high such that the 11 sequences could be aligned with little ambiguity. The missing codons in ONMV were all near the CP amino-terminus, a region that is also variable among WSMV isolates. Given the codon based alignment, several non-uniform patterns of divergence between and within the two virus species became apparent. Within species transitions (ts) are about 4-fold more frequent than transversions (tv) while between WSMV and ONMV the ts/tv ratio is 1.1. This indicates that one or both branches leading to their common ancester may be longer than lengths based on the number of nt differences alone. The two species differ by an average of 106 aa replacements out of a total of 527 codons. The vast majority (86%) of replacement codons have nt substitutions in multiple codon positions, and even 14 of 217 silent codons involved multiple nt substitutions. Further, only 54 aa replacements between ONMV and WSMV were at sites monomorphic in the WSMV data set. Thus, it seems that the rate of evolution varies widely among sites for these two viruses and that not all substitution events are independent of each other.

Last Modified: 10/21/2014
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