rRNA is depleted by rRNA-to-probe hybridization, RNase H digestion, and DNaseI digestion steps. The retained mRNA and other non-coding RNA can be used for LncRNA and other non-coding RNAs analysis. This kit contains digestion probes targeting of mitochondrial rRNA and chloroplast rRNA. It can efficiently remove major rRNAs from a variety of plant species and provide the most informative sequencing results. This kit is applicable for both intact and degraded RNA samples. The resulting rRNA-depleted RNA is suitable for RNA library construction and other downstream experiments.