Haplotype-resolved genome and multi-omics landscape reveal an epigenetic regulation of citric acid accumulation in lemon

Abstract Lemon (Citrus limon L.), an economically important Citrus species, produces high levels of citric acid. However, the regulatory mechanisms underlying citric acid accumulation in lemon fruit are poorly understood. In this study, we generated a haplotype-resolved genome for ‘Eureka’, a widely cultivated commercial lemon cultivar. Based on the progenitor sequences, we elucidated the origin and identified some domesticated loci of the lemon haplomes, including those associated with citric acid metabolism. Comparative genomics analysis revealed that the gene families enriched in the pathways related to stress responses and soluble sugar biosynthesis were dramatically contracted in the lemon genome. Substantial allelic variations in sequences, gene expression and methylation levels were detected between the two haplotypes. Of note, transcript levels of vacuolar P-ATPases, PH5, encoding a proton pump involved in citric acid accumulation, were drastically higher in Eureka lemon relative to sweet lemon, which contains trace amount of citric acid in the fruit. In addition, whole-genome bisulfite sequencing revealed that the promoter of PH5 was highly methylated in sweet lemon but not in Eureka. Furthermore, demethylation of the PH5 promoter led to an increase in the citric acid content. Taken together, these findings demonstrate that low DNA methylation level in the promoter region of PH5 contributes to the abundant accumulation of citric acid in lemon fruit. Our study provides a valuable genetic resource for investigating the domestication mechanism in citrus and underpins genome-based genetic engineering to create either acid or acidless cultivars.