Unlocking the Genetic Blueprint of Maize Leaf Development Through Spatial Long-Read Isoform Sequencing
Understanding maize leaf development is crucial for global food security. Overcoming the limitations of traditional short-read sequencing, the genomics research team led by Dr. Mei-Yeh Jade Lu, in collaboration with Dr. Wen-Hsiung Li at the Biodiversity Research Center, Academia Sinica, pioneered the integration of high-resolution spatial transcriptomics and long-read isoform sequencing to depict the transcriptome landscape of maize embryonic leaf development.
This multi-omics study successfully unlocked the tissue-specific expression patterns of gene isoforms across distinct stages of embryonic leaf vein development, resolving vascular structures at unprecedented developmental resolution. Leveraging these long-read transcriptome isoforms, the team constructed a flagship maize genome annotation database—MaizeV5_IsoAnn—which uncovers 5,228 novel genes and hundreds of previously unannotated functional long non-coding RNAs (lncRNAs). Importantly, these long-read-annotated gene models significantly enhance expression detection across thousands of genes, including key transcription factors (TFs) that were previously underrepresented.
By integrating multi-omics datasets with in situ validations, the study decodes the spatial regulatory network of the key vascular factor LBD26, revealing the regulatory circuitry governing leaf vein development alongside its upstream transcription factors and downstream target genes. This groundbreaking dataset offers a vital resource for the global maize community, while establishing an adaptable methodological framework that is broadly applicable across diverse plant systems, including single-cell and spatial researches.
This work was achieved by the first author Dr. Wye-Lup Kong at the Biodiversity Research Center, Academia Sinica, with Dr. Mei-Yeh Jade Lu and Dr. Wen-Hsiung Li serving as corresponding authors, in collaboration with Dr. Chi-Chih Wu, Dr. Yao-Ming Chang, and the team members of NGS High Throughput Genomics Core. The research was published in Nature Plants (DOI: 10.1038/s41477-026-02364-y; online publication: August 17th, 2026).
The study was supported by the Academia Sinica Core Facility and Innovative Instrument Project (AS-CFII-111-216).
