Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato

Abstract

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 (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.

Acknowledgements

This work was supported by grants from the Fundamental Research Funds for the Central Universities (KYCXJC2022003), the National Natural Science Foundation of China (32070243), and the Outstanding Young Teacher of the QingLan Project of Jiangsu Province. Y.V.d.P. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (833522) and from Ghent University (Methusalem funding, BOF.MET.2021.0005.01). The computational resources and services were provided by the Bioinformatics Center of Nanjing Agricultural University.

Author contributions

J.Y.X., Z.Q.S., F.C., and Y.V.d.P. conceived the study. Z.Q.S. and Z.Z. collected plant samples. H.Y.F. conducted genome assembly and annotation. H.Y.F., Z.Z., S.Y.H., Y.J.C., X.R.M., and S.X.L. conducted analyses of RNA-seq data. Y.H.Z. constructed the database. J.Y.X. and Z.Q.S. drafted the manuscript. All authors read the manuscript and participated in the revision of the manuscript. All authors approved the final manuscript.

Data availability

The data supporting the findings of this work are available within the paper and its supplementary information files. The datasets generated and analyzed during this study are available from the corresponding author upon request. All sequencing data generated have been deposited in National Genomics Data Center (https://bigd.big.ac.cn/) with BioProject ID PRJCA012325 under GSA CRA008482. The genome assembly, along with the gene models, the functional annotation, and some supplementary information files are available on FigShare at the link: (https://doi.org/10.6084/m9.figshare.21509817). All this information can also be accessed under GWH: WGS029763 and MicroTomBase (http://eplant.njau.edu.cn/microTomBase).

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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