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United States Department of Agriculture

Agricultural Research Service

Title: Sequence Space Explored by a Wheat Streak Mosaic Virus Population

Authors
item STENGER, DRAKE
item French, Roy
item Seifers, Dallas - KANSAS STATE UNIVERSITY

Submitted to: American Society for Virology Meeting
Publication Type: Abstract Only
Publication Acceptance Date: February 15, 2002
Publication Date: July 25, 2002
Citation: Stenger, D.C., French, R.C., Seifers, D. 2003. Sequence space explored by a wheat streak mosaic virus population. American Society For Virology Meeting. (Not published by meeting)

Technical Abstract: Polymorphism within a collection of 58 wheat streak mosaic virus isolates was examined. A 1267 nt region encompassing the coat protein (CP) cistron and flanking sequences was amplified by RT-PCR. Consensus sequences for each isolate were derived from three clones per RT-PCR product. Among 59 consensus sequences (one isolate was a mixture), only two were identical. Clades A-C contained divergent isolates from Mexico (Clade A), the Czech Republic, Hungary, and Russia (Clade B), and Iran (Clade C). Fifty-four closely related consensus sequences of isolates from the US (51), Canada (1), and Turkey (2) comprised Clade D. Maximum pair-wise nt divergence within Clade D was 3.6 percent. In contrast, pair-wise nt divergence between two of the most distantly related sequences (Sidney 81 of Clade D and El Batan 3 of Clade A) was 20 percent. Nonetheless, the proportion of variable sites within Clade D (21.4 percent) was similar to that of the Sidney 81 - El Batan 3 pair (20 percent). Patterns of total polymorphism within Clade D and the Sidney 81 - El Batan 3 pair were remarkably similar with respect to synonymous, nonsynonymous, and non-coding substitutions, as were the proportions of substitutions as a function of nt position within codons. The majority of substitutions within Clade D were silent and randomly distributed. Nonsynonymous substitutions exhibited a clumped distribution. Over half of the variable sites within Clade D were of allele size class 1, suggesting that the isolates are evolving independently and in a nondeterministic manner, within the constraints of selection. These results indicate that Clade D has undergone substantial and, most likely, recent divergence with the majority of substitutions predicted as neutral with respect to fitness.

Last Modified: 7/25/2014
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