## 5 Conclusions  
In this study, higher total phenol and flavonoid contents were detected in the stage 1 of yellow-peel pitaya pulps during fruit development. A higher content of ascorbic acid was detected in 'WCHL' pitaya than 'YCHL' pitaya. Starch was mainly accumulated at early stages and transferred to soluble sugars at S5. Six sugars components (glucose, sucrose, fructose, galactose, inositol, and sorbitol) and six organic acids (oxalic, malic, fumaric, glyceric, succininic, citric and citramalic acid) were detected in pitayas. Glucose and malic acid were the key factors contributed to the taste and flavor quality of 'WCHL' pitaya. Sucrose, fructose, and glucose were the main sugars, and citric acid was the dominant acid responsible for fruit quality of 'YCHL' pitaya. Based on the expression profilings, 27 candidate genes probably involved in ascorbate biosynthesis and regeneration were achieved, of which _PMIs_ was vital for ascorbic acid synthesis, and _APXs_ and _MDHRs_ played important roles in ascorbate accumulation. A total of 32 candidate genes probably involved in starch synthesis and degradation pathway were isolated, of which _AGPSs_ were key genes for starch synthesis and _AMY_, _BAM_ and _PHSs_ were key regulators controlling starch degradation. _SPSs Ivrs_, _SuSys_, _HXKs_, _FRKs_ and _PGI_ coordinately regulated sucrose, fructose, and glucose synthesis, of which _SuSys_ and _FRKs_ were expressed more than the other genes. Organic acids were lowly accumulated in ripening stages associated with downward expression patterns of _PGK_, _Enos_, _PEPCs_, _PKs_, and _PDHs_ which limited the carbon flux into TCA cycle. Twenty candidate genes involved in organic acid production and degradation (TCA cycle) were obtained in pitayas. The findings of this study provide basic information for improving fruit quality of yellow-peel pitaya. **Supplementary Materials:** The following supporting information can be downloaded at [[https://www.mdpi.com/article/10.3390/plants11050694/s1](https://www.mdpi.com/article/10.3390/plants11050694/s1)]([https://www.mdpi.com/article/10.3390/plants11050694/s1](https://www.mdpi.com/article/10.3390/plants11050694/s1)), Figure S1: The RT-qPCR analyses of eleven candidate genes (A-K) in sugar and acid metabolic pathway and the coefficient analyses between FPKM values and RT-qPCR of those genes (L); Table S1: RNA-Seq data and corresponding quality control information; Table S2: Specific primers used in RT-qPCR assay; Table S3: The transcript abundance of genes related to ascorbate pathways in 'WCHL' and 'YCHL' pitayas pulps; Table S4: Correlation analyses between the ascorbic acid contents and expression patterns of candidate genes in 'WCHL' and 'YCHL' pitayas; Table S5: The transcript abundance of genes related to starch synthesis and degradation pathways in 'WCHL' and 'YCHL' pitayas; Table S6: Correlation analyses between the starch contents or total soluble sugar and expression patterns of candidate genes in 'WCHL' and 'YCHL' pitayas; Table S7: The transcript abundance of genes related to major sugar biosynthesis pathways in 'WCHL' and 'YCHL' pitayas; Table S8: Correlation analyses between the main sugar contents and expression patterns of candidate gene in 'WCHL' and 'YCHL' pitayas; Table S9: The transcript abundance of genes related to TCA cycle pathways in 'WCHL' and 'YCHL' pitayas; Table S10: Correlation analyses between the main organic acid contents and expression patterns of candidate genes in 'WCHL' and 'YCHL' pitayas. **Author Contributions:** Conceptualization, F.X, J.C. ([PERSON]) and Y.Q. ; Methodology and validation, F.X and C.C. ; Formal analysis, investigation, resources, data curation and visualization, F.X, C.C, J.C. ([PERSON]), Y.Y., Q.H., Z.Z., J.Z. and G.H. ; Writing--original draft preparation, F.X. ; Supervision, J.C. ([PERSON]) and Y.Q. ; Project administration, Y.Q. ; Funding acquisition, J.C. ([PERSON]) and Y.Q. All authors have read and agreed to the published version of the manuscript.