A comparison of total RNA extraction methods for RT-PCR based differential expression of genes from Trichoderma atrobrunneum

Abstract

The genus Trichoderma is ubiquitous in various niches and is currently used for biocontrol, biofertilizer, enzyme production and bioremediation. However, molecular mechanisms underlying its diverse biological functions are yet not fully elucidated. Extraction of high-quality RNA for downstream applications such as quantitative polymerase chain reaction is a prerequisite. The current study aims to optimize a total RNA extraction protocol for high-quality and quantity RNA from Trichoderma atrobrunneum. Seven RNA extraction protocols including Trizol, RiboEx PureLink RNA mini kit, high salt CTAB (cetyltrimethylammonium bromide), modified high salt CTAB, SDS (sodium dodecyl sulfate) and CTAB-PVP (polyvinylpyrrolidone) were performed separately, to extract RNA. Quality and quantity of extracted RNA samples were further analyzed by Nanodrop spectrophotometry, agarose gel electrophoresis and RT-PCR analysis. The results of quantitative and qualitative analysis of RNA samples showed that more intact, high-quality RNA was extracted using the modified high salt CTAB as compared to other methods. The RT-PCR results for the amplification of the genes encoding β-tubulin and Ubiquitin carrier protein also showed lowest threshold cycle (Ct) and coefficient of variation (CV) for RNA samples extracted with the modified high salt CTAB method as compared to RNA samples extracted with other protocols. Therefore, it is proposed that the modified high salt CTAB protocol is an excellent method to obtain high-quality RNA with good yield from T. atrobrunneum for its downstream applications. Moreover, the optimized protocol is very economical and can be used to extract total RNA from a large number of samples.