Genes Associated with the Accumulation of Proanthocyanidins in Nelumbo nucifera Gaertn

Proanthocyanidins are a subclass of flavonoids formed through a poorly understood polymerization process that forms chains of 3–30 catechins and epi-catechins. Proanthocyanidins serve as UV protectants and antifeedants that accumulate in diverse plant species, including the lotus. To identify candidate genes underlying proanthocyanidin synthesis and polymerization, we generated and functionally annotated transcriptomes from seedpods and seed epicarps of two lotus cultivars, “Guoqing Hong” and “Space Lotus”, which accumulate markedly divergent proanthocyanidin levels across the immature, near-mature, and mature developmental stages. Our transcriptome analysis was based on a total of 262.29 GB of raw data. We aligned the transcriptome data with the lotus genome and obtained an alignment efficiency that ranged from 91.74% to 96.44%. Based on the alignment results, we discovered 4774 new genes and functionally annotated 3232 genes. A total of 14,994 differentially expressed genes (DEGs) were identified from two-by-two comparisons of transcript libraries. We found 61 DEGs in the same developmental stage in the same tissue of different species. Comparative transcriptome analysis of seedpods and seed epicarps from two cultivars identified 14,994 differentially expressed genes (DEGs), of which 10 were functionally associated with proanthocyanidin synthesis and 9 were possibly implicated in the polymerization reactions. We independently quantified the expression of the candidate genes using qRT-PCR. Significant differences in the expression of candidate genes in different tissues and periods of lotus species are consistent with particular genes contributing to the polymerization of catechins and epi-catechins into proanthocyanidins in lotus seedpods and seed epicarps.