Abstract
The past breeding efforts have created purple leaf tea varieties for better health benefits, such as ‘Zijuan’. To understand mechanisms behind the purple trait, the genome of ZJ was assembled using PacBio and Hi-C technologies. The assembled genome size was approximately 3.06 Gb that formed 1,344 scaffolds, in which the scaffold N50 size was approximately 214.76 Mb. Besides, 99.12% of the assembled sequences were anchored on 15 chromosomes. The LTR assembly index (LAI) was 17.67, indicating the high quality of the assembled genome.
The analysis of structural variations (SVs) was completed via comparing the genomes of ZJ and green leaf ‘Shuchazao’ (SCZ). The results revealed 51,507 SVs, which were related to 16,551 genes including CsMYB75 and 27 other genes involved in anthocyanin biosynthesis. The results showed that the expression level of CsMYB75 was enhanced in ZJ. RT-qPCR data verified that the expression of CsMYB75 was significantly higher in the purple leaves of ZJ than in the green leaves of LJ43 and YK10. Based on these data, we hypothesized that the SV led to the activation of CsMYB75. The results disclosed that the CsMYB75’s SV resulted from a 181 bp insertion localized at the 153 bp upstream of the start codon ATG and 181 bp after the TATA-box in its promoter. To characterize this insertion, we further mined the TEs of ZJ genome through ReapeatMasker software and identified that the 181 bp insertion was a part of Copia LTR. The activation of CsMYB75 by its purpleTE augmented the anthocyanin biosynthesis in the leaves of ZJ. The 181 bp purpleTE enhanced the activity of the CsMYB75’s promoter.
In summary, the genome assembly has identified a 181 bp purpleTE inserted in the CsMYB75’s promoter of purple leaf tea cultivars. The purpleTE is an enhancer that increases the activity of the CsMYB75’s promoter, the CsMYB75’s transcript, and protein abundance. The function of the purpleTE shows a genetic mechanism turning tea leaves from evergreen to purple color and provides a strategy for engineering new traits.
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