**5. Conclusions**

In summary, this study generated tremendous genomic and metabolic resources and elucidated the mechanisms of the differential anthocyanin accumulation in purple and green turnips. It provides an important theoretical basis for further in-depth analysis of the candidate structural genes along with the key transcription factors predicted to modulate anthocyanins in turnip towards developing new turnip varieties with improved nutritional quality.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/18/ 4387/s1. Table S1. Statistics of the read mapping results. GP (Green Turnip) and PT (Purple Turnip); Table S2. Quantification of the detected anthocyanins in two turnips. GP (Green Turnip) and PT (Purple Turnip) and S1–S5 represent the different developmental stages. Data from three biological replicates are shown; Table S3. List of the shared and stage-specific differentially accumulated anthocyanins between Green Turnip and Purple Turnip at different developmental stages S1–S5; Table S4. The primer sequences of genes used for quantitative real time PCR.

**Author Contributions:** H.Z. and H.W. designed the research and drafted the manuscript. H.Z., Q.L. and Z.T. performed the research. Q.W., H.H. and H.L. collected samples in the field. H.Z., Y.M. prepared plant materials and carried out qRT-PCR analysis. All authors read and approved the final manuscript.

**Funding:** This research was funded by the National natural Science Foundation of China (grant number: 31960600) and the Project of Renovation Capacity Building for the Young Sci-Tech Talents Sponsored by Xinjiang Academy of Agricultural Sciences (grant number: xjnkq-2019003).

**Acknowledgments:** We thank Biomarker Technologies Corporation (Beijing, China) for assistance with the PacBio RSII platform and Metware Biotechnology Co., Ltd. (Wuhan, China) for the self-compiled metabolite database MWDB.

**Conflicts of Interest:** The authors declare no conflict of interest.
