Xue, Jia-YuFan, Hai-YunZeng, ZhenZhou, Yu-HanHu, Shuai-YaLi, Sai-XiCheng, Ying-JuanMeng, Xiang-RuChen, FeiShao, Zhu-QingVan de Peer, Yves2024-07-102024-07-102023-09Xue, J.Y., Fan, H.Y., Zeng, Z et al. 2023, 'Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato', Horticulture Research, vol. 10, no. 9, pp. 1-11. https://DOI.org/10.1093/hr/uhad147.2052-727610.1093/hr/uhad147http://hdl.handle.net/2263/96911MicroTom 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 want to adopt MicroTom as a model plant for research.en© The Author(s) 2023. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.GenomeRNAomeMicroTomPlant-microbe interactionsMetabolismOrgan developmentSDG-15: Life on landArticle