As　an　internal　modification　of　transcripts,　RNA　methylation　determines　RNA　fate　by　changing　RNA–protein　binding　affinity.　In　plants,　RNA　methylation　is　ubiquitous　and　is　involved　in　all　aspects　of　RNA　post-transcriptional　regulation.　For　instance,　long-distance　mobile　RNAs,　strongly　influenced　by　their　methylation　status,　play　important　roles　in　plant　growth,　development　and　environmental　adaptation.　Cucumber/pumpkin　heterografts　are　widely　used　to　improve　stress　tolerance　of　cucumber　and　to　study　mobile　RNA　signals　due　to　their　strong　developed　vasculature　system.　Here,　we　developed　the　Cucume　(Cucurbit　RNA　methylation,　http://cucume.cn/)　database　for　these　two　important　vegetables,　cucumber　(Cucumis　sativus　L.)　and　pumpkin　(Cucurbita　moschata)　with　high　productivity　worldwide.　We　identified　mRNAs　harboring　5-methylcytosine　(m5C)　and　N6-methyladenosine　(m6A)　sites　in　pumpkin　and　cucumber　at　the　whole　genome　level　via　Methylated　RNA　Immunoprecipitation　sequencing　(MeRIP-seq)　of　different　tissues　and　the　vascular　exudates.　In　addition　to　RNA　methylation　sites,　the　Cucume　database　includes　graft-transmissible　systemic　mRNAs　identified　in　previous　studies　using　cucumber/pumpkin　heterografts.　The　further　integration　of　cucumber　genome-wide　association　analysis　(GWAS)　and　quantitative　trait　loci　(QTL)　allows　the　study　of　RNA　methylation-related　genetic　and　epigenetic　regulation　in　cucurbits.　Therefore,　the　here　developed　Cucume　database　will　promote　understanding　the　role　of　cucurbit　RNA　methylation　in　RNA　mobility　and　QTL,　ultimately　benefitting　future　breeding　of　agronomic　crop　germplasms.　©　2023　The　Authors