plosone-phylo
pone.0032772.g005.png
Microdiversity of the F10 lineage population of Pond-1.
The genetic diversity of the twelve F10 lineage strains isolated from Pond-1 over a period of four years (2003–2007) is illustrated. Left panel. NJ tree based on concatenated nucleotide sequences of twelve loci (Table S4) with a total length of 9031 alignment positions. Middle panel. Only three out of 13 sequenced loci showed sequence polymorphism. The icd2 and Pnuc_1095 genes were present with two alleles differing in the sequenced parts in total in eight and seven positions (polymorphic positions), respectively. Numbers depict the total numbers of polymorphic sites (first number) and the number of non-synonymous sites (second number) among the polymorphic sites. The locus Pnuc_1240 of strain P1-Kol5 differed from all other sequenced strains in the presence of an insertion element (IS, insertion sequence). Sequences of Pnuc_1240 were not considered in the calculation of the presented phylogenetic tree. Right panel. Results from genetic fingerprinting with the independent methods RAPD (Ziemke A), ERIC, and REP-PCR. Each method resulted in different fingerprints, but each method revealed basically only two types of fingerprints (G1a and G1b). The REP-PCR fingerprint G1b* differed only weakly from G1b. Colors green and red indicate that the respective strains share or do not share, respectively, a particular trait with the genome-sequenced strain QLW-P1DMWA-1.
pone.0032772.g005.png
Microdiversity of the F10 lineage population of Pond-1.
The genetic diversity of the twelve F10 lineage strains isolated from Pond-1 over a period of four years (2003–2007) is illustrated. Left panel. NJ tree based on concatenated nucleotide sequences of twelve loci (Table S4) with a total length of 9031 alignment positions. Middle panel. Only three out of 13 sequenced loci showed sequence polymorphism. The icd2 and Pnuc_1095 genes were present with two alleles differing in the sequenced parts in total in eight and seven positions (polymorphic positions), respectively. Numbers depict the total numbers of polymorphic sites (first number) and the number of non-synonymous sites (second number) among the polymorphic sites. The locus Pnuc_1240 of strain P1-Kol5 differed from all other sequenced strains in the presence of an insertion element (IS, insertion sequence). Sequences of Pnuc_1240 were not considered in the calculation of the presented phylogenetic tree. Right panel. Results from genetic fingerprinting with the independent methods RAPD (Ziemke A), ERIC, and REP-PCR. Each method resulted in different fingerprints, but each method revealed basically only two types of fingerprints (G1a and G1b). The REP-PCR fingerprint G1b* differed only weakly from G1b. Colors green and red indicate that the respective strains share or do not share, respectively, a particular trait with the genome-sequenced strain QLW-P1DMWA-1.