[Transcriptome dataset comparing the initial development of swollen stem versus non-swollen basal stem (root-stem...

The economic value of Brassica juncea var. tumida depends on the yield and quality of its swollen stem (known as Qingcaitou). However, the frequent lodging of the stem base during early swelling causes the plant to grow prostrate, severely limiting mechanical harvesting. This data paper presents a transcriptome dataset constructed primarily from RNA-seq data, supplemented by histological, physiological, biochemical, and molecular validation data, to compare the initial development between the swollen stem and the non-swollen basal stem (root-stem node). The core components of this dataset include RNA-seq raw reads (FASTQ files) for both stem types. The accompanying validation data consist of histological parameters (cross-sectional area, diameter, phloroglucinol-stained area, and cell compactness), physiological indices (lignin and hemicellulose content), and qRT-PCR validation results for key lignin biosynthesis genes (BjuCCoAOMT1 and BjuHCT). The data show that while the swollen stem exhibits advantages in morphological traits such as cross-sectional area and diameter, its phloroglucinol-stained area, cell compactness in stained regions, and lignin and hemicellulose content are significantly lower than those in the root-stem node. Moreover, the root-stem node shows significantly upregulated expression of key lignin biosynthesis genes and specifically activated phenylpropanoid and flavonoid biosynthesis pathways. This dataset reveals quantitative differences in lignin deposition and related gene expression between the two stem types and provides a fundamental resource for molecular marker screening, research on lodging resistance mechanisms, and breeding of varieties suitable for mechanical harvesting.