The researchers combined metabolite measurements with gene-expression data to investigate how amino acid accumulation changed during fruit development in the two cultivars. Their analysis linked chemical patterns observed at each stage with candidate genes potentially involved in amino acid biosynthesis. By examining both cultivars across the same developmental stages, the study compared the timing and scale of metabolic changes as the fruits ripened.

K-means clustering of the metabolite data revealed pronounced stage-specific temporal shifts in black mulberry. White mulberry showed a comparatively stable accumulation profile. Within the white cultivar, early-stage clusters were primarily associated with growth-related metabolites, whereas late-stage clusters were enriched in metabolites related to fruit-flavor development.

These patterns indicate that the two cultivars differed not only in amino acid composition but also in how metabolite profiles changed over the ripening period. Transcriptome analysis identified differential expression of the genes HK, PGAM, ENO and PK, together with transcription factors from the NAC, ERF, bHLH, MYB and WRKY families that may be associated with amino acid biosynthesis. Correlation analysis between transcript and metabolite data was then used to examine potential regulatory relationships.

The results connected changes in gene expression with changes in amino acids and related metabolites during development, but they establish associations rather than proving that any individual gene or transcription factor directly caused a particular metabolic difference. The research provides a molecular and chemical description of amino acid biosynthesis diversity between two mulberry cultivars. Its findings offer a basis for the development of amino acid-based nutritional supplements and mulberry-derived functional foods, as stated by the authors.

Subject of Research: Comparative metabolomic and transcriptomic analysis of amino acid accumulation during mulberry fruit development

Article Title: Integrated transcriptomic and metabolomic analysis reveals the amino acid biosynthesis diversity in black and white mulberry

Article References: Sun, Z., Zhang, W., Ma, W., Zhang, R., kumar, R. M. S., Huang, C., & Li, J. (2026). Integrated transcriptomic and metabolomic analysis reveals the amino acid biosynthesis diversity in black and white mulberry. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09692-3

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09692-3

Keywords: mulberry fruit, amino acids, metabolomics, transcriptomics, fruit ripening, black mulberry, white mulberry, gene expression, plant metabolism, biosynthesis, Integrated, transcriptomic