Rosette leaves of about one-month-old plants were collected and subject to DNA extraction with CTAB method followed by bisulfite DNA conversion using the EpiTect Bisulfite kit (QIAGEN) kit. Three regions of the FWA gene were amplified from the converted DNA with Pfu Turbo Cx (Agilent): Region 1 (chr4: 13038143-13038272), Region 2 (chr4: 13038356- 13038499) and Region3 (chr4: 13038568-13038695). Primers used are listed in Supplementary Table 4 . Libraries were prepared with the purified PCR product by the Kapa DNA Hyper Kit (Roche) together with TruSeq DNA UD indexes for Illumina (Illumina) and were sequenced on Illumina iSeq 100 or HiSeq 4000 instruments.
BS-PCR-seq data was analyzed as previously described43 (link). Briefly, raw reads were aligned to both strands of the TAIR10 reference genome with BSMAP (v.2.90)66 (link) allowing up to 2 mismatches and 1 best hit. After quality filtering, the methylation level of cytosines was calculated as the ratio of C/(C+T), and customized R scripts were used to plot methylation data over the FWA region 1-3.
BS-PCR-seq data was analyzed as previously described43 (link). Briefly, raw reads were aligned to both strands of the TAIR10 reference genome with BSMAP (v.2.90)66 (link) allowing up to 2 mismatches and 1 best hit. After quality filtering, the methylation level of cytosines was calculated as the ratio of C/(C+T), and customized R scripts were used to plot methylation data over the FWA region 1-3.
