The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

Abstract

Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence time between H. undatus and C. gigantea was estimated to be 9.18 MYA. Functional enrichment analysis of orthologous gene clusters (OGCs) in six Cactaceae plants found significantly enriched OGCs in drought resistance. Fruit flavor-related functions were overrepresented in OGCs that are significantly expanded in H. undatus. The H. undatus draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage time. Lastly, genes of the betacyanin (a red-violet pigment and antioxidant with a very high concentration in dragon fruits) biosynthetic pathway were found to be co-localized on a 12 Mb region of one chromosome. The consequence may be a higher efficiency of betacyanin biosynthesis, which will need experimental validation in the future. The H. undatus draft genome will be a great resource to study various cactus plants.

The influence of the fortification of red pitaya (Hylocereus polyrhizus) powder on the in vitro digestion, physical parameters, nutritional profile, polyphenols and antioxidant activity in the oat‐wheat bread

“…Pitaya fruit is a rich source of antioxidants (i.e. betacyanins, flavonoids and phenolic acids), prebiotics, polysaccharides, vitamins, dietary fibre and minerals (Ca, Fe, Mg, Na, P and Zn) (Zheng et al ., 2021). These bioactive compounds regulate glycaemic response, lipid accumulation in liver, reduce inflammation and growth of foodborne pathogens due to high radical scavenging abilities and modulation of gut microbiota (Song et al ., 2016; Zambrano et al ., 2019; Saenjum et al ., 2021).…”

Polyphenol Utilization Proteins in the Human Gut Microbiome

“…Table 2 shows the top 10 Pfam domains ranked by their occurrence in non-PUPs. To statistically test their overrepresentation in the 1,074 PGCs, a hypergeometry test was conducted on each of the 10 Pfam domains, with proteins in PGCs as the foreground and all the proteins of the 989 PGC-containing genomes as the background, following a method described in our previous papers ( 35 – 38 ). All these 10 Pfam domains have very significant P values, suggesting that compared to the genome background, they tend to appear in PGCs (or colocalized with known PUP homologs).…”

Identification of Allergens in White- and Red-Fleshed Pitaya (Selenicereus undatus and Selenicereus costaricensis) Seeds Using Bottom-Up Proteomics Coupled with Immunoinformatics

“…mRNA sequences of the predicted allergens were obtained from the European Nucleotide Archive (ENA) database. The mRNA sequences were BLAST-searched against the S. undatus genome (assembly ASM1758966v1 in the NCBI genome database) [ 16 ] for determining whether genes encoding predicted allergens were presented. The BLAST results are shown in Table 5 .…”