ARS | Publication request: USE OF COALESCENT-BASED METHODS TO INFER RATES OF INSTRASPECIFIC RECOMBINATION IN RNA PLANT VIRUSES

Submitted to: American Phytopathological Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: March 15, 2003
Publication Date: June 1, 2003
Citation: FRENCH, R.C., STENGER, D.C. USE OF COALESCENT-BASED METHODS TO INFER RATES OF INSTRASPECIFIC RECOMBINATION IN RNA PLANT VIRUSES. AMERICAN PHYTOPATHOLOGICAL SOCIETY ANNUAL MEETING. 2003. Phytopathology 93 (Supplement) S27

Technical Abstract: Phylogenetic analysis of sequences from multiple isolates of plant viruses often reveals a radial tree topology with little bootstrap support for internal nodes. A star-like tree for coat protein sequences of a collection of 49 U. S. isolates of wheat streak mosaic virus (WSMV) was partly due to homoplasy, which may result from recurrent mutation or a history of recombination. Under coalescent theoretical framework one may calculate the relative likelihood of recombination given the observed number and sample frequencies of biallelic polymorphic sites. The inferred recombination rate for WSMV was much higher than the population mutation rate. For comparison, recombination rates were estimated for sample sets of coat protein gene sequences from GenBank for 34 barley yellow dwarf PAV isolates, 67 cucumber mosaic virus (CMV) isolates, and 26 yam mosaic virus (YMV) isolates. Apparent recombination rates for YMV and CMV were similar to WSMV while that of PAV was at least 10-fold lower. These results suggest that recombination can be an important factor affecting the genetic structure of plant RBA virus populations.