Zea mays subsp. mays Raw sequence reads. Zea mays subsp. mays

Transcript end maturation is important for organellar gene expression, and mapping of RNA termini is a key step to unravel the underlying mechanism. However, limitation of current RNA mapping methods impedes the molecular study of organellar transcript end maturation in plants. Here, we take inspiration from circular RNA (circRNA), and establish the high-throughput transcript end mapping system (Hitens) together RNA 5-polyphsophatase treatment, in vitro RNA circularization, circRNA sequencing and the circRNA identification algorithm MeCi. With Hitens, the full sequences of 5,751 and 76,789 transcripts are determined in maize plastid and mitochondrion, respectively, corresponding to 1,162 and 13,757 high-confidence termini. Using these termini, 55 mature mRNAs, 10 precursor mRNAs, 31 intron splicing products, and 64 non-coding RNAs are identified in maize organelles, and these RNAs are experimentally verified. ZmRNaseII is dually targeted to plastid and mitochondrion, and the Hitens results show it is required for 3-end formation of nearly all mRNAs in plastid but only atp1 and atp4 mRNAs in mitochondrion.