RNA-seq Analysis of Anthocyanin Biosynthesis in Strawberry

Total RNA was extracted from ripe flesh of two cultivars (Xiaobai and Benihoppe) using a quick RNA isolation kit (Tiangen Biotech, Beijing, China). Libraries were constructed using a NEBNext^® Ultra™ RNA Library Prep Kit (New England Biolabs, Beverly, MA, USA) and sequenced on an Illumina HiSeq™ 2500. Raw reads were filtered to exclude low-quality reads and adaptors. Clean reads were mapped to Fragaria x ananassa Camarosa Genome by hisat2 (Kim et al., 2019 (link)). The expression levels of anthocyanin biosynthesis pathway genes and R2R3-MYB genes in each RNA-seq library were measured using the TPM method. Differentially expressed genes (DEGs) was obtained by DESeq2 through TPM normalization, and padj < 0.05 was selected as the threshold.