PT - JOURNAL ARTICLE AU - Jia-Yu Xue AU - Hai-Yun Fan AU - Zhen Zeng AU - Yu-Han Zhou AU - Shuai-Ya Hu AU - Sai-Xi Li AU - Ying-Juan Chen AU - Fei Chen AU - Yves Van de Peer AU - Zhu-Qing Shao TI - Extensive RNA editing in tomato nuclear genes AID - 10.1101/2022.12.01.518646 DP - 2022 Jan 01 TA - bioRxiv PG - 2022.12.01.518646 4099 - http://biorxiv.org/content/early/2022/12/04/2022.12.01.518646.short 4100 - http://biorxiv.org/content/early/2022/12/04/2022.12.01.518646.full AB - Sequence discrepancy between genomic DNA and transcribed RNAs, namely RNA editing (RE), was reported to be extensive in metazoan nuclear genomes and plant organellar genomes, but largely unexplored in plant nuclear genomes. By comparing the tomato microTom RNA-seq data to its newly assembled genome, we, for the first time, detected extensive RE events (37,984 sites in 5,873 genes) on in the plant nuclear genome, which is supported by evidence from both experimental validation and proteomic data. Other than the prevalence of RE in the microTom genome, the biased pattern-transition overwhelmingly outnumbering transversion-rivals that in animals, and may imply an ancient and shared mechanism underlying RE across eukaryotes. We observed conserved RE sites that were always edited under all conditions, and could be considered as "fixed mutations" at the RNA level; also we detected conditional RE sites occurring only in specific organ/developmental stage/treatment, possibly suggesting distinct functional roles. Evolutionarily, RE results in sequence diversity at the RNA level and may lead to even functional innovation of proteins, hence may be considered as an additional mechanism to expand gene diversity other than gene duplications and alternative splicing.Competing Interest StatementThe authors have declared no competing interest.