Genome-Wide Analysis of the BBX Gene Family and Their Drought Stress Responses in the Gymnosperm Torreya grandis

B-BOX (BBX) transcription factors regulate plant growth and drought tolerance, whereas comprehensive characterization of BBX gene families in gymnosperms remains scarce. We identified 13 TgBBXs in Torreya grandis at the genome-wide level, and phylogenetic analysis grouped them into five subgroups consistent with the conserved classification of plant BBX members. Promoter analysis revealed abundant light hormone and stress related cis-elements, and the TgBBXs displayed distinct expression patterns across various tissues and reproductive developmental stages. PEG-triggered drought decreased leaf chlorophyll, accompanied by increased root H2O2, APX and POD levels. Transcriptome data showed obvious tissue-specific expression and organ-dependent drought responses; most of TgBBX5–TgBBX12 were continuously upregulated in leaves under PEG treatment, whereas several members declined in roots. WGCNA further indicated that the MEturquoise module, which contained most TgBBXs, was closely associated with chlorophyll accumulation and antioxidant responses. Among these genes, TgBBX2, TgBBX7, and TgBBX13 with module membership over 0.9 are putative hub genes, and their associated genes enrich in photosynthesis and antioxidant pathways. This study systematically characterized the BBX family in T. grandis for the first time and identified key drought-responsive genes, providing valuable resources for drought-tolerant molecular breeding of this economically important gymnosperm.