In a study published in New Phytologist, researchers from Xishuangbanna Tropical Botanical Garden (XTBG) of the Chinese Academy of Sciences identified and characterized over 113,700 long noncoding RNA (IncRNA) genes across seven economically vital Solanaceae plant species. They provided the first large-scale, multidimensional functional framework for these enigmatic genetic elements in this plant family.

Researchers identified and described lncRNAs from seven species of Solanaceae plants through large-scale specific strand RNA sequencing (ssRNA-seq). They first conducted data acquisition based on high-throughput sequencing technology, and then processed the data using bioinformatic tools including sequence conservation analysis, expression profile analysis, epigenetic modification analysis, and comparison of lncRNAs with protein-coding genes.

Using uniform computational pipelines on ssRNA-seq data, researchers identified 113,700 lncRNA genes from seven species: cultivated tomato, potato, eggplant, pepper, tobacco, and wild tomato.

In tomato, 97.4% of lncRNAs have been annotated with basic sequence, expression, conservation, and epigenetic signal annotations. And 25.7% of tomato lncRNAs were further predicted to be involved in critical biological processes like stress response, development, and metabolism.

Compared with protein-coding genes, IncRNAs exhibited distinct features including greater tissue specificity, unique stress response patterns, different sequence compositions, and specific epigenetic signal distributions like histone modifications. It was predicted that 1,158 lncRNAs are 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.

"By integrating multi-omics data–transcriptomics, epigenomics, comparative genomics, we have built a comprehensive, multidimensional framework that moves beyond simple identification. We have also shown how to link lncRNAs to potential functions using this integrated approach," explained LIU Changning from XTBG.