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Camellia sinensis cv. 'Yanling Huayecha' (YHC) is an albino-green chimaeric tea mutant with stable genetic traits. Here, we analysed the cell ultrastructure, photosynthetic pigments, amino acids, and transcriptomes of the albino, mosaic, and green zones of YHC. Well-organized thylakoids were found in chloroplasts in mesophyll cells of the green zone but not the albino zone. The albino zone of the leaves contained almost no photosynthetic pigment. However, the levels of total amino acids and theanine were higher in the albino zone than in the mosaic and green zones. A transcriptomic analysis showed that carbon metabolism, nitrogen metabolism and amino acid biosynthesis showed differences among the different zones. Metabolite and transcriptomic analyses revealed that (1) downregulation of CsPPOX1 and damage to thylakoids in the albino zone may block chlorophyll synthesis; (2) downregulation of CsLHCB6 , CsFdC2 and CsSCY1 influences chloroplast biogenesis and thylakoid membrane formation, which may contribute to the appearance of variegated tea leaves; and (3) tea plant variegation disrupts the balance between carbon and nitrogen metabolism and promotes the accumulation of amino acids, and upregulation of CsTSⅠ and CsAlaDC may enhance L-theanine synthesis. In summary, our study provides a theoretical basis and valuable insights for elucidating the molecular mechanisms and promoting the economic utilization of variegation in tea. • CsPPOX1 , CsLHCB6 , CsFdC2 and CsSCY1 downregulation and thylakoid damage in albino zone may cause variegated tea leaves. • Tea plant variegation disrupts the balance between carbon and nitrogen metabolism and promotes amino acids accumulation. • Upregulation of CsTSⅠ and CsAlaDC may enhance theanine synthesis. [ABSTRACT FROM AUTHOR]

• Transcriptome, translatome, and metabolome were used to analyse tea etiolation. • Ribosome profiling reveals carbon and phytohormone metabolism mediate leaf etiolation. • HY5 inhibited chlorophyll and flavonoids metabolism in etiolated leaf. • Changes in gene structure between EL and GL influence their gene expression. Albino tea plants (Camellia sinensis , Atps) are among the most attractive germplasm resources because of their unique phenotype and flavor. Although previous studies have extensively investigated the transcriptional and metabolic mechanisms in Atps, the lack of research at the translational level hinders the understanding of translation control and multi-omics integration. Here, we integrated the transcriptome, translatome, and metabolome to study the global translation and its effect on the metabolic characteristics of Atps. Comparative analysis of RNA-seq and Ribo-seq datasets indicated that 4,295 genes were expressed as synergic responses in etiolated leaves and were mainly enriched in the carbon metabolism and phytohormone pathways. Further integration-omics analyses revealed that the HY5 gene was upregulated at both the transcription and translation levels and repressed chlorophyll biosynthesis and flavonoids metabolism due to low levels of indole acetic acid and auxin response factors. Moreover, sequence characterizations (guanine-cytosine (GC) content, length, and normalized minimal free energy (NMFE)) highly influenced the translational efficiencies (TE) of genes and upstream open reading frames (uORFs), and a higher quantity of uORFs and TE were observed in EL, inhibiting the expression of downstream genes. In summary, we demonstrated that translation regulation contributes to causing leaf color variation and provided a valuable method for exploring the potential regulatory mechanisms controlling phytohormones that affect crop quality using multi-omics technology. [Display omitted] [ABSTRACT FROM AUTHOR]