*4.5. Identification of Transcription Factors and TEs*

Transcription factors and transcriptional regulatory factors were predicted and classified from the assembled transcriptome data according to Pérez-Rodríguez et al. [105] and Jin et al. [106]. In addition, the DEG sequences were screened for transcription factors using the iTAK tool (http://bioinfo.bti. cornell.edu/tool/itak), a program to identify plant transcription factors and transcriptional regulators and protein kinases, which currently provides both online and standalone versions with a hidden Markov model [107].

TEs were identified from the reference genome using RepeatMasker (http://www.repeatmasker. org/). TE density based on the length ratio of each bin within every chromosome was displayed as a Circos plot [48]. TEs annotated within gene set domains (including 2-kb upstream and downstream sequences) of DMR-related genes overlapping with DEGs were used for DNA methylation analysis. TEs were classified, and their distributions and mC contexts were analyzed.
