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Fig. 3 | BMC Genomics

Fig. 3

From: Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils

Fig. 3

Comparative analysis of with closest sequenced relatives. (a) Sequence identity between newly sequenced strains and closest relatives, with 16S rDNA (black), rpoB gene (dark grey) and multilocus sequence comparison (light grey) shown for each pair of strains. (b) Genomic location of alignment gaps larger than 100 bp. Grey ring represents newly sequenced genomes, with high-confidence and putative BGCs labeled as in Fig. 1. Outer ring shows location of extra sequence present in closest relative but missing in our newly sequenced strain. Inner ring shows location of extra sequence present in newly sequenced strains but missing from closest relative. (c) SNP analysis of strain GS93–23 and its closest relative ISP-5461. Pie-chart in upper right shows relative proportion of silent, missense, and nonsense mutations. Circle chart at left shows frequency of all SNPs found in CDSs, with the outer ring showing one-letter code for amino acids, colored according to chemical property (hydrophobic, orange; hydrophilic, green; basic, blue; acidic, pink). Three-base code is shown using three inner rings, with innermost representing the first codon position and outermost representing the last codon position. For each codon, there are two nodes on the graph. In the clockwise direction, the first node corresponds to a codon in GS93–23 and the second node to ISP-5461. Each CDS SNP is represented by an arc connecting a codon in GS93–23 to a codon in ISP-5461, with the width of the arc indicating number of instances of that mutation. (d) Location of SNPs relative to CDS position. Top line graph shows enrichment of SNPs upstream of start codons using absolute positions, with the solid blue line showing average value for a sliding 3-base window and the light-blue filled region showing one standard deviation in either direction. Bottom line graph shows SNP abundance versus relative position in CDS, where relative position equals absolute position divided by CDS length. Black line and grey boxes show average SNP abundance and 1-, 2-standard deviations as calculated for the last 90% of the CDS. CDS: coding DNA sequence; SD: Shine-Dalgarno sequence

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