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Article|19 Jul 2023|OPEN
Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato 
Jia-Yu Xue1 ,† , Hai-Yun Fan1 ,† , Zhen Zeng2 ,† , Yu-Han Zhou1 , Shuai-Ya Hu1 , Sai-Xi Li2 , Ying-Juan Cheng1 , Xiang-Ru Meng1 , Fei Chen3,4 , and Zhu-Qing Shao2 , , Yves Van de Peer,1,5,6 ,
1College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
2State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
3College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Haikou 570228, China
4Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
5Department of Plant Biotechnology and Bioinformatics, VIB-UGent Center for Plant Systems Biology, Ghent University, B-9052 Ghent, Belgium
6Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
*Corresponding author. E-mail:,,
Jia-Yu Xue,Hai-Yun Fan and Zhen Zeng contributed equally to the study.

Horticulture Research 10,
Article number: uhad147 (2023)
Views: 64

Received: 03 Feb 2023
Accepted: 15 Jul 2023
Published online: 19 Jul 2023


MicroTom 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 ( 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.