HD-Zip, a special class of transcription factors in high plants, has a role in plant development and responding to external environmental stress. Heat stress has always been an important factor affecting plant growth, quality, and yield. Carotenoid content is also an important factor affecting the color of the inner leaf blades of Chinese cabbage. In this study, the genomes of three Brassicaceae plants were selected: Chinese cabbage (Brassica rapa subsp. pekinensis), Brassica oleracea, and Brassica napus. We identified 93, 96, and 184 HD-Zip genes in the B. rapa, B. oleracea, and B. napus, respectively. The HD-Zip gene family was classified into four subfamilies based on phylogeny: I, II, III, and IV;. The results of cis-acting element analysis suggested that HD-Zip family genes may participate in various biological processes, such as pigment synthesis, cell cycle regulation, defense stress response, etc. Conserved motifs prediction revealed that three motifs exist among the four HD-Zip gene families and that different motifs exhibit significant effects on the structural differences in HD-Zips. Synteny, Ks, and 4DTv results displayed that genome-wide triplication events act in HD-Zip gene family expansion. Transcriptome data showed that 18 genes responded (>1.5-fold change) to heat stress in Chinese cabbage, and 14 of 18 genes were from the HD-Zip I subfamily. Three genes had up-regulation, and eight genes had down-regulation in high-carotenoid-content Chinese cabbage. The BraA09g011460.3C expression level was up-regulated after heat stress treatment and significantly reduced in varieties with high carotenoid content, indicating its potential for heat stress tolerance and carotenoid content regulation. This study provided important gene resources for the subsequent breeding of Chinese cabbage.

The sugar content in watermelon significantly influences its flavor. To understand the sugar accumulation pattern in small-fruited watermelon and identify candidate genes involved in sugar synthesis and conversion, we measured the sugar content (sucrose, fructose, and glucose) at five developmental stages: 10d, 16d, 22d, 28d, and 34d post-pollination. Two watermelon varieties with the largest sugar content difference at 28d post-pollination (high-sugar G38-28 and low-sugar 482276-28) were selected for transcriptome sequencing. Differentially expressed genes (DEGs) were validated using RT-qPCR. Additionally, the sugar contents of three commercial varieties (‘Su Meng NO.5’, ‘Su Meng NO.6’, ‘Su Meng NO.7’) and their parents were compared at five stages. Results showed glucose and fructose levels peaked between 22d and 28d, followed by a decrease, while sucrose content continuously increased. F1 hybrids exhibited glucose and sucrose trends similar to their paternal parent and fructose trends similar to their maternal parent. Transcriptome sequencing identified 9337 DEGs (5072 upregulated and 4265 downregulated). Gene Ontology analysis highlighted overrepresentation in categories such as pectinase and oxidoreductase activity. KEGG analysis identified 12 DEGs involved in sugar synthesis and conversion pathways, including phenylpropanoid biosynthesis and pentose and glucuronate interconversions. RT-qPCR validation corroborated the transcriptome data. These findings explain the distinct sugar accumulation patterns in G38-28 and 482276-28 at the transcriptional level, offering insights for genetic breeding and regulation of key sugar-related genes in watermelon.