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bioRxiv · 10.1101/2022.12.01.518646

Extensive RNA editing in tomato nuclear genes

Xue, J.-Y.·Fan, H.-Y.·Zhen, Z.·Zhou, Y.-H.·Hu, S.-Y.·Li, S.-X.·Chen, Y.-J.·Chen, F.·Van de Peer, Y.·Shao, Z.-Q.
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Abstract

MicroTom tomato has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g., arbuscular mycorrhizal symbiosis and fruit development. Additionally, non-coding RNAs, including miRNAs, lncRNAs and circRNAs were also identified, together with their potential targets. Interacting networks between different types of non-coding RNAs (miRNA-lncRNA), and non-coding RNAs and genes (miRNA-mRNA and lncRNA-mRNA) were constructed as well. Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit. Lastly, we established a database (http://eplant.njau.edu.cn/microTomBase/) with genomic and transcriptomic data, as well as details of gene co-expression and interacting networks on microTom, and this database should be of great value to those who wants to adopt microTom as a model plant for research.

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Xue, J.-Y., Fan, H.-Y., Zhen, Z., Zhou, Y.-H., Hu, S.-Y., Li, S.-X., Chen, Y.-J., Chen, F., Van de Peer, Y., Shao, Z.-Q.. 2022-12-03. Extensive RNA editing in tomato nuclear genes. https://doi.org/10.1101/2022.12.01.518646

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