Genetic variation of populations of Citrus psorosis virus, by S. Martín, M. L. García, A. Troisi, L. Rubio, G. Legarreta, O. Grau, D. Alioto, P. Moreno and J. Guerri
Journal of General Virology vol. 87, part 10, pp. 3097 - 3102
Supplementary Table S1. Primers used for RT-PCR amplification. [PDF] (22 KB)
Supplementary Material
Analysis of RNA recombination events. The statistical significance of incongruent phylogenetic groupings was assessed with the RETICULATE program (Sneath et al., 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. P values for non-randomness of genetic incompatibility were significant (P<0.02) for the analyses of concatenated regions R1–R2 (P=0.0003), R1-R3 (P=0.0001) and R2–R3 (P=0.0057), indicating that phylogenetically incompatible positions are not randomly distributed and thus providing evidence for genetic exchange. P values were not significant when R1, R2 and R3 sequences were analysed separately [R1 (P=0.2020), R2 (P=0.3727) and R3 (P=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.
Analysis of nucleotide conservation in R3 segment. 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.
References
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