Selection of proper reference genes for the cyanobacterium Synechococcus PCC 7002 using real-time quantitative PCR

Abstract

Synechococcus sp. PCC 7002 is known to be tolerant to most of the environmental factors in natural habitats of Cyanobacteria. Gene expression can be easily studied in this cyanobacterium, as its complete genome sequence is available. These properties make Synechococcus sp. PCC 7002 an appropriate model organism for biotechnological applications. To study the gene expression in Cyanobacteria, real-time quantitative PCR (qPCR) can be used, but as this is a highly sensitive method, data standardization is indicated between samples. The most commonly used strategy is normalization against internal reference genes. Synechococcus sp. PCC 7002 has not yet been evaluated for the best reference genes. In this work, six candidate genes were analyzed for this purpose. Cyanobacterial cultures were exposed to several stress conditions, and three different algorithms were used for ranking the reference genes: geNorm, NormFinder, and BestKeeper. Moreover, gene expression stability value M and single-control normalization error E were calculated. Our data provided a list of reference genes that can be used in qPCR experiments in Synechococcus sp. PCC 7002.

Keywords: Synechococcus sp. PCC 7002; UV-B irradiation; microaerobiosis; real-time quantitative PCR; reference genes.