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Journal of Virology, June 2004, p. 6666-6675, Vol. 78, No. 12
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.12.6666-6675.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Molecular Population Genetics of Cucumber Mosaic Virus in California: Evidence for Founder Effects and Reassortment

Han-Xin Lin,1,{dagger} Luis Rubio,2 Ashleigh B. Smythe,3 and Bryce W. Falk1*

Department of Plant Pathology,1 Department of Nematology, University of California—Davis, Davis, California 95616,3 Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain2

Received 5 November 2003/ Accepted 18 February 2004

The structure and genetic diversity of a California Cucumber mosaic virus (CMV) population was assessed by single-strand conformation polymorphism and nucleotide sequence analyses of genomic regions 2b, CP, MP, and the 3' nontranslated region of RNA3. The California CMV population exhibited low genetic diversity and was composed of one to three predominant haplotypes and a large number of minor haplotypes for specific genomic regions. Extremely low diversity and close evolutionary relationships among isolates in a subpopulation suggested that founder effects might play a role in shaping the genetic structure. Phylogenetic analysis indicated a naturally occurring reassortant between subgroup IA and IB isolates and potential reassortants between subgroup IA isolates, suggesting that genetic exchange by reassortment contributed to the evolution of the California CMV population. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that different coding regions and even different parts of coding regions were under different evolutionary constraints, including a short region of the 2b gene for which evidence suggests possible positive selection.

* Corresponding author. Mailing address: Department of Plant Pathology, University of California, 1 Shields Ave., Davis, CA 95616. Phone and fax: (530) 752-0302. E-mail: bwfalk{at}ucdavis.edu.

{dagger} Present address: Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.

Journal of Virology, June 2004, p. 6666-6675, Vol. 78, No. 12
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.12.6666-6675.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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