1887

Abstract

(CPsV), the type species of genus , has a segmented, negative-stranded RNA genome. We examined the population structure and genetic variation of CPsV in three coding regions located in RNAs 1, 2 and 3, analysing 22 isolates from Argentina, California, Florida, Italy and Spain. Most isolates contained a predominant sequence and some minor variants. Estimations of the genetic diversity and phylogenetic clustering of isolates disclosed two populations, one comprising isolates from Spain, Italy, Florida and California and the other including the Argentinean isolates. Isolate CPV-4 (from Texas) included for comparison was distant from both groups, suggesting that it belongs to a third group. The low ratio between non-synonymous and synonymous nucleotide substitutions indicated strong selection for amino acid sequence conservation, particularly in the coat protein gene. Incongruent phylogenetic relationships in different genomic regions suggested that exchange of genomic segments may have contributed to CPsV evolution.

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2006-10-01
2020-01-24
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vol. , part 10, pp. 3097 - 3102

Primers used for RT-PCR amplification. [PDF](22 KB)

The statistical significance of incongruent phylogenetic groupings was assessed with the RETICULATE program (Sneath , 1975; Jakobsen & Easteal, 1996), which analysed the phylogenetic incompatibility between pairs of informative positions in alignments of the concatenated nucleotide sequences of R1, R2 and R3 regions, scored against a set of 10,000 randomized alignments. values for non-randomness of genetic incompatibility were significant ( <0.02) for the analyses of concatenated regions R1–R2 ( =0.0003), R1-R3 ( =0.0001) and R2–R3 ( =0.0057), indicating that phylogenetically incompatible positions are not randomly distributed and thus providing evidence for genetic exchange. values were not significant when R1, R2 and R3 sequences were analysed separately [R1 ( =0.2020), R2 ( =0.3727) and R3 ( =0.3119)] and, therefore, no evidence was found for recombination within each region. To search for potential ancestors of recombinant sequences, we also performed a conversion analysis of the concatenated R1–R2–R3 regions using the program GENECONV (Sawyer, 1989), which estimates whether two sequences of a set of aligned sequences show identical consecutive polymorphic sites more frequently than expected in a random distribution.

To test whether the low variation at synonymous nucleotide positions (dS value) of the R3 region, in comparison with the R1 and R2 regions, was due to synonymous codon usage bias, the effective number of codons (ENC) (Wright, 1990) was calculated independently for each region using the program DNASP (Rozas & Rozas, 1999). The ENC ranges from 20 if only one codon is used for each amino acid to 61 if all synonymous codons are equally used.

A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. , 291–295. A highly sensitive heminested RT-PCR assay for the detection of citrus psorosis virus targeted to a conserved region of the genome. , 15–22. DNASP version 3: an integrated program for molecular population genetic and molecular evolution analysis. , 174–175. Statistical tests for detecting gene conversion. , 526–538. Detecting evolutionary incompatibilities from protein sequences. , 311–332. The "effective number of codons" used in a gene. , 23–29.



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