Evaluation of commercially available small RNA methods for plant samples

Plant small RNAs are a diverse and complex set of molecules, ranging in length from 21 to 24 nt, involved in a wide range of essential biological processes. Nowadays, high-throughput sequencing is the most commonly used method for the discovery and quantification of small RNAs. However, it is known that several biases can occur during the preparation of small RNA libraries, especially using low input RNA. We used two types of plant biological samples to evaluate the performance of seven commercially available methods for small RNA library construction, using different RNA input amounts. We show that when working with plant material, library construction methods have differing capabilities to capture small RNAs, and that different library construction methods provide better results when applied to the detection of microRNAs, phased small RNAs, or tRNA-derived fragments. In this study we include 96 small RNAseq samples, made with seven different commercially available kits, two types of RNA samples ( pre-meiotic and meiotic anthers from maize) and four different RNA input amounts (1000ng, 100ng, 10ng and 1ng). All the samples include three technical replicates.