Journal: PLoS ONE

Article Title: Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity

doi: 10.1371/journal.pone.0000917

Figure Lengend Snippet: Unrooted, consensus phylogenetic trees were obtained from 2,000,000 generations of the Markov chain Monte Carlo simulation in Bayesian analysis using a general time-reversal model of nucleotide substitution . The number above each branch indicates the Bayesian posterior probability. The scale bars represent 0.1 expected substitutions per site. Branch lengths are proportional to evolutionary distance. Sequences were aligned using ClustalX and subsequently manually aligned prior to the Bayesian phylogenetic analysis. A, Known CTV genomes and CTV genomes assembled from resequencing analysis of FS2-2 (highlighted orange). The suffix at the end of fs2_2 distinguishes multiple genotypes in the isolate and also indicates the anchor sequence from which the consensus contig was generated by the Phrap program. B, the 5′ proximal 1 kb, and C, p33-coding region of CTV genomes obtained by direct sequencing of RT-PCR clones. In both B and C, Bayesian posterior probability and clones with identical sequences were omitted for clarity. Recombinant sequences are highlighted in green.

Article Snippet: Sequence fragments and the associated quality scores generated by GDAS were converted into fasta-format files and used to assemble full and partial CTV genomic contigs using the Phrap program implemented in the CodonCode Aligner (CodonCode, Dedham, MA).

Techniques: Sequencing, Generated, Reverse Transcription Polymerase Chain Reaction, Clone Assay, Recombinant