Identification, characterization, and design of plant genome sequences using deep learning

Due to its excellent performance in processing large amounts of data and capturing complex non-linear relationships, deep learning has been widely applied in many fields of plant biology. Here we first review the application of deep learning in analyzing genome sequences to predict gene expression, chromatin interactions, and epigenetic features (open chromatin, transcription factor binding sites, and methylation sites) in plants. Then, current motif mining and functional component design and synthesis based on generative adversarial networks, large models, and attention mechanisms are elaborated in detail. The progress of protein structure and function prediction, genomic prediction, and large model applications based on deep learning is also discussed. Finally, this work provides prospects for the future development of deep learning in plants with regard to multiple omics data, algorithm optimization, large language models, sequence design, and intelligent breeding.