In a study published in New Phytologist, researchers from Xishuangbanna Tropical Botanical Garden (XTBG) of the Chinese Academy of Sciences have systematically identified and characterized over 113,700 long noncoading RNA (IncRNA) genes across seven economically vital Solanaceae plant species, including tomato, potato, pepper, and eggplant. It provides the first large-scale, multidimensional functional framework for these enigmatic genetic elements in this crucial plant family.

The researchers utilized large-scale specific strand RNA sequencing (ssRNA-seq) technology to uniformly identify and systematically describe lncRNAs from seven species of Solanaceae plants. They first conducted data acquisition based on high-throughput sequencing technology, followed by the processing and analysis of the data using bioinformatic tools, including sequence conservation analysis, expression profile analysis, epigenetic modification analysis, and comparison of lncRNAs with protein-coding genes (PCGs).

Using uniform computational pipelines on large-scale strand-specific RNA-seq data, the researchers identified 113,700 lncRNA genes from seven species: cultivated tomato, potato, eggplant, pepper, tobacco, and wild tomatoes.

For tomato, 97.4% of lncRNAs now have basic sequence, expression, conservation, and epigenetic signal annotations. Crucially, 25.7% of tomato lncRNAs were predicted to be involved in critical biological processes like stress response, development, and metabolism.

IncRNAs exhibited distinct features compared to protein-coding genes, including greater tissue specificity, unique stress response patterns, different sequence compositions, and specific epigenetic signal distributions (like histone modifications).

The researchers predicted that 1,158 lncRNAs potentially involved in fruit development and ripening, a key functional trait for Solanaceae crops.

The study revealed, for the first time in plants, significant tissue-specific fluctuations in epigenetic marks (like histone modifications) at lncRNA loci, providing a new mechanism to understand and predict their tissue-specific functions.

"This research provides a desperately needed roadmap," explained LIU Changning. "By integrating multi-omics data–transcriptomics, epigenomics, comparative genomics–we've built a comprehensive, multidimensional framework that moves beyond simple identification. We've shown how to link lncRNAs to potential functions, like fruit ripening, using this integrated approach."

First published: 01 June 2025