Study Identifies Reliable Reference Genes for Gene Expression in Bougainvillea Bracts

Researchers integrating genome-anchored transcriptome screening with multi-algorithm stability analysis have identified and validated dedicated reference genes for gene expression studies in Bougainvillea bracts. The investigation demonstrated that specific internal control genes provide reliable normalization in specialized ornamental tissues, while also uncovering expression dynamics of candidate genes involved in bract color development.

Bougainvillea species are prized for their colorful bracts, but conducting accurate gene expression studies in these specialized organs has been hampered by a lack of stably expressed reference genes.

To address this limitation, the authors evaluated three published transcriptome datasets to isolate candidate normalizers. A total of ten candidate reference genes were selected based on predefined expression-level and stability criteria, establishing a focused panel for subsequent testing across different plant tissues.

The expression stability of the candidate genes was systematically assessed across non-bract tissues, bracts, and total samples using five algorithms: Delta-Ct, BestKeeper, geNorm, NormFinder, and RefFinder. Across non-bract tissues and total samples, S12-L, 1F1A, and Actin proved to be the most stable reference genes. In bract tissues specifically, S12-L, MBF, and Actin ranked as the most stable candidates. Furthermore, geNorm analysis indicated that two reference genes are sufficient for non-bract tissues, whereas three reference genes are required for accurate normalization in bracts.

Biological validation confirmed the functional importance of selecting validated reference genes. Utilizing the stable normalizer S12-L generated consistent expression patterns for the target genes LOG3 and LOG5. In contrast, the use of unstable candidate reference genes led to biased gene expression estimates, underscoring the necessity of using verified reference sets.

Applying S12-L as a normalizer, the researchers investigated candidate CHS genes associated with bract colour development. Five of seven candidate CHS genes exhibited a biphasic expression pattern during bract development in the tested cultivar, which was accompanied by an organ color transition from deep yellow to white. This developmental pattern correlated with anthocyanin reduction, a metabolic flux shift toward colorless flavonols, and chlorophyll degradation.

The study provides validated candidate reference genes to support future molecular research on bract development in the tested Bougainvillea cultivar. In addition, the authors highlighted that the integrated screening strategy offers a useful workflow for identifying reference genes in other specialized organs of ornamental plants.

Subject of Research: Reference gene validation for Bougainvillea bracts

Article Title: Genome-anchored transcriptome-based screening and validation of dedicated reference genes for Bougainvillea spp. bracts

Article References: Gan, R., Zhu, Z., Han, Y., Rao, D., Li, T., Wu, E., Cui, Y., Cao, J., & Chen, Y. (2026). Genome-anchored transcriptome-based screening and validation of dedicated reference genes for Bougainvillea spp. bracts. BMC Genomics. https://doi.org/10.1186/s12864-026-13532-x

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13532-x

Keywords: Bougainvillea, reference genes, gene expression, bract development, transcriptome screening, Actin, CHS genes, Genome-anchored, transcriptome-based, screening, validation, dedicated