Long non-coding RNAs (lncRNAs) have been gradually verified as functional regulator participating in plants, yet their functions remain underexplored, especially in the Solanaceae family. While substantial progress has been made in identifying lncRNAs in different Solanaceae species, systematic functional annotations are lacking. In this study, we uniformly identified and systematically characterized lncRNAs from seven Solanaceous species using large-scale strand-specific RNA-seq (ssRNA-seq). About 113700 lncRNA genes were obtained and analyzed from their sequence, conservation, expression profile, dynamic epigenetic signals and genetic mutants. In tomato, 97.4% of lncRNAs have been annotated with basic characteristics. 25.7% of the lncRNAs were further predicted to be involved in stress response, developmental processes and metabolic pathways. Comparisons between lncRNAs and protein-coding genes (PCGs) highlighted unique characteristics in tissue expression, stress responses, sequence composition, and epigenetic signal distribution. Taking the process of fruit development and ripening as an example, we further mined the data resources and predicted a total of 1,158 lncRNAs associated with this process, presenting how our curated data resources can be utilized to discover the functions of plant lncRNAs. Overall, this study provides a comprehensive multi-dimensional framework for lncRNA functional research, which serves as a valuable reference for understanding lncRNA functions in other plants.

We categorized our curated datasets into five major sections on the website, including transcriptomic sample and epigenomic sample information, lncRNA sequences, transcriptomic expression matrices for lncRNA genes and protein-coding genes in each species, conservation information of Solanaceae lncRNAs, and functional annotation details of tomato lncRNAs. Each file is accessible for download and is accompanied by detailed instructions for usage in each section.The Search module on the website enables comprehensive retrieval of lncRNA information through gene ID queries, displaying multi-dimensional features. If you are interested into our research, please click the following categories to explore!

If you encounter any issues or have suggestions, please contact yangwenjing@xtbg.ac.cn.

In this section, we provide 1,616 samples, including transcriptomic and epigenomic data. For each sample, detailed descriptions and references are available. All transcriptomic sample libraries are strand-specific, as checked by RESQC analysis.

Sample information download : BS-seq ; ChIP-seq ; RNA-seq

In this part, the fasta format files of lncRNAs identified in seven species (S. lycopersicum, S. pimpinellifolium, S. pennellii, S. tuberosum, C. annuum, S. melongena and N. tabacum) are available for download.

LncRNA sequences download : Capsicum annuum ; Nicotiana tabacum ; Solanum lycopersicum ; Solanum melongena ; Solanum pennellii ; Solanum pimpinellifolium ; Solanum tuberosum ;

The transcriptomic expression matrices of the seven species display the expression levels (FPKM) of lncRNA genes and protein-coding genes across multiple samples. The descriptive information for the samples is provided in the "Sample information" section. Please note that each expression matrix has not been normalized. If normalization is required, we recommend using the data_norm method from the GCEN software.

Gene expression matrix download : Capsicum annuum ; Nicotiana tabacum ; Solanum lycopersicum ; Solanum melongena ; Solanum pennellii ; Solanum pimpinellifolium

We provide the sequence conservation information of Solanaceae lncRNAs across various plants, as well as the syntenic conservation information of Solanaceae lincRNAs among species within the Solanaceae family.

Sequence conservation download : Capsicum annuum ; Nicotiana tabacum ; Solanum lycopersicum ; Solanum melongena ; Solanum pennellii ; Solanum pimpinellifolium ; Solanum tuberosum

Synteny conservation download : Capsicum annuum ; Nicotiana tabacum ; Solanum lycopersicum ; Solanum melongena ; Solanum pennellii ; Solanum pimpinellifolium ; Solanum tuberosum

The annotations of S. lycopersicum lncRNAs are categorized into three main types: Sequence, Expression, and Genomic signal.

Sequence includes TE-associated, MiRNA_precursors, PhasiRNA_precursors, and Conserved-eTMs.

Expression includes Stress, GO/KEGG, CeRNA, Cis-acting, Trans-acting, Metabolic-related, and Mutant.

Genomic signal includes TF-binding (Transcript factors enrichment by ChIP-seq analysis), Diff-peak (a significant alteration in the enrichment level of H3K4me3 or H3K27me3 in fruits compared to the leaves), and DMR (a significant decrease in the level of differential methylation regions in fruits compared to leaves).

Annotation information download : Solanum lycopersicum