Figure 3
Relative quantification of genes from the potentially duplicated region in the SRMK07 strain’s genome. For this, five reference single-copy genes (‘R1’ to ‘R5’ defined below) and eight genes (‘T1’ to ‘T8’ defined below) from the potentially duplicated region in the SRMK07 strain’s genome were first selected for the qPCR experiments. A gene ‘R1’ encoding NADH-quinone oxidoreductase subunit H (5,392,720–5,393,685 bp in the NRRL 5491 genome) was used as a control to measure the relative quantity of the other four single-copy genes (blue bars), and the eight genes from the potentially duplicated region (red bars). Genes ‘R2’, ‘R3’, ‘R4’, and ‘R5’ are those known to exist as a single copy across Streptomyces species, and encode the following proteins, respectively (along with the chromosome location in the NRRL 5491 genome): RtcB family protein (5,488,049–5,488,159 bp); RNA helicase (5,756,656–5,760,582 bp); aspartate kinase (6,341,319–6,342,599 bp); and type I DNA topoisomerase (6,399,363–6,402,227 bp). Genes ‘T1’, ‘T2’, ‘T3’, ‘T4’, ‘T5’, ‘T6’, ‘T7’, and ‘T8’ from the potentially duplicated region encode the following proteins, respectively: 3-ketoacyl-CoA thiolase (9,778,772–9,809,242 bp); regulatory protein AfsR (9,875,692–9,877,524 bp); l-lysine cyclodeaminase (9,900,735–9,901,766 bp); ferredoxin (9,904,048–9,904,284 bp); glycerol uptake operon antiterminator regulatory protein (10,001,392–10,002,039 bp); hypothetical protein (10,003,629–10,004,255 bp); SDR family oxidoreductase (10,035,843–10,036,631 bp); and putative ABC transporter ATP-binding protein YbiT (10,693,310–10,694,929 bp). ‘T1’ and ‘T8’ represent the start and end regions of the potentially duplicated region. ‘T3’, ‘T4’ and ‘T6’ belong to rapamycin BGC. The primers used for these qPCR experiments are available in Supplementary Table S2. The presented data represent the mean from triplicate experiments, and the error bars indicate standard deviations.
