Fig. 2

Transcriptome-wide m⁶A methylation profiles in tomato fruit. a Venn diagrams showing the overlap of m⁶A peaks identified in three independent m⁶A-seq experiments on wild-type (WT) fruit at 39 DPA and 42 DPA and Cnr fruit at 42 DPA. Rep, replicate; DPA, days post-anthesis. Only the peaks identified in all three biological replicates were regarded as confident peaks and used for subsequent data analysis. b Gene Ontology (GO) analysis of the biological process, molecular function, and cellular component for the m⁶A-containing transcripts identified in m⁶A-seq. c Proportions of the m⁶A-modified transcripts containing different m⁶A peak numbers. Error bars represent the standard deviation of three different m⁶A-seq experiments. d Examples of m⁶A-modified transcripts containing one m⁶A peak, two m⁶A peaks, and three m⁶A peaks in WT fruit at 42 DPA. The black dot line rectangles indicate the positions of m⁶A peaks, which are named as peaks 1–6. The blue lines indicate the positions of amplification fragments in the following m⁶A-immunoprecipitation (IP)-qPCR. e Validations of the m⁶A peaks shown in d by m⁶A-IP-qPCR. Data are presented as mean ± standard deviation (n = 3)