Integrating transcriptomic and metabolomic analyses to investigate the impact of magnesium on the growth and development of tobacco plants

Tobacco ( Nicotiana tabacum L.), is an important industrial crop contributing to economic growth and tax revenue. Magnesium (Mg) is essential for plant growth and development, affecting yield and quality, yet its molecular response mechanisms in tobacco remain unclear. In this study, six Mg treatments (M1–M6) were tested; M5 yielded the highest biomass and best photosynthesis. Elevated Mg increased nitrogen, potassium, and sulfur uptake, while reducing iron, zinc, copper, and manganese absorption. Leaf ultrastructure revealed that Mg deficiency caused starch granule accumulation and impaired chloroplast development. Transcriptome analysis revealed that Mg deficiency induced expression of the magnesium ion transporter Nta12g21110, and VIGS experiments showed that silencing this gene reduced photosynthesis. Magnesium deficiency resulted in the up-regulation of 12 serine/arginine-rich splicing factors, promoting alternative splicing events. Among these, the Nta15g05470 gene (encoding chaperone protein dnaJ 13) and the Nta17g23880 gene (encoding glucose-6-phosphate/phosphate translocator 2) exhibited skipped exon and alternative 3′ splice site splicing types, respectively. These splicing events are involved in the stress response to magnesium deficiency. Integrated transcriptome and metabolome analyses highlighted enrichment in starch and sucrose metabolism and phenylpropanoid biosynthesis pathways. Mg deficiency increased soluble sugars in shoots but limited their root transport and raised coniferin levels, enhancing stress tolerance. This study elucidates the primary metabolic pathways influencing plant growth and development under varying Mg supply levels. The findings offer a theoretical foundation for the application of Mg fertilization. • Mg dose-dependently affected photosynthesis. • The magnesium transporter protein Nta12g21110 played a critical role in regulating magnesium homeostasis and exerts a significant influence on photosynthetic efficiency. • Mg deficiency significantly affectde starch and sucrose metabolism and phenylpropanoid biosynthesis pathway. • Mg deficiency induced the accumulation of sucrose, coniferin, and other related metabolites.