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

Zheng, Jie; Meinhardt, Lyndel W.; Goenaga, Ricardo; Zhang, Dapeng; Yin, Yanbin

doi:10.1038/s41438-021-00501-6

Cited by 36 publications

(31 citation statements)

References 107 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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).…”

Section: Introductionmentioning

confidence: 99%

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

Huang

Kasapis

et al. 2021

Int J of Food Sci Tech

View full text Add to dashboard Cite

This study evaluated the physical parameters, polyphenol profile and antioxidant activity before and after the in vitro digestion of red pitaya powder‐enriched oat‐wheat bread compared to plain wheat bread, oat‐wheat bread and red pitaya powder. The enrichment of red pitaya powder significantly increased the polyphenol, mineral contents, insoluble dietary fibre, firmness and moisture content of oat‐wheat bread compared to wheat bread, while contributed to a minor reduction in bread volume and dough extensibility due to gluten dilution. The oat‐wheat bread was found to have the lowest predicted glycaemic response, but 5%, 10% and 15% red pitaya powder formulated oat‐wheat bread showed a significantly lower glycaemic response than plain wheat bread as well as red pitaya powder.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Huang

Kasapis

et al. 2021

Int J of Food Sci Tech

View full text Add to dashboard Cite

show abstract

“…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).…”

Section: Resultsmentioning

confidence: 99%

Polyphenol Utilization Proteins in the Human Gut Microbiome

Zheng

Zhang

et al. 2022

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

Dietary polyphenols can significantly benefit human health, but their bioavailability is metabolically controlled by human gut microbiota. To facilitate the study of polyphenol metabolism for human gut health, we have manually curated experimentally characterized polyphenol utilization proteins (PUPs) from published literature. This resulted in 60 experimentally characterized PUPs (named seeds) with various metadata, such as species and substrate. Further database search found 107,851 homologs of the seeds from UniProt and UHGP (Unified Human Gastrointestinal Protein) databases. All PUP seeds and homologs were classified into protein classes, families and subfamilies based on Enzyme Commission (EC) numbers, Pfam (protein family) domains and sequence similarity networks. By locating PUP homologs in the genomes of UHGP, we have identified 1,074 physically linked PUP gene clusters (PGCs), which are potentially involved in polyphenol metabolism in the human gut. The gut microbiome of Africans was consistently ranked the top in terms of the abundance and prevalence of PUP homologs and PGCs among all geographical continents. This reflects the fact that dietary polyphenols are more commonly consumed by African population than other populations such as Europeans and North Americans. A case study of the Hadza hunter-gatherer microbiome verified the feasibility of using dbPUP to profile metagenomic data for biologically meaningful discovery, suggesting an association between diet and PUP abundance. A Pfam domain enrichment analysis of PGCs identified a number of putatively novel PUP families. Lastly, a user-friendly web interface ( https://bcb.unl.edu/dbpup/ ) provides all the data online to facilitate the research of polyphenol metabolism for improved human health. Importance Long-term consumption of polyphenol-rich foods have been shown to lower the risk of various human diseases such as cardiovascular diseases, cancers, and metabolic diseases. Raw polyphenols are often enzymatically processed by gut microbiome, which encode various polyphenol utilization proteins (PUPs) to produce metabolites with much higher bioaccessibility to gastrointestinal cells. This study delivered dbPUP as an online database for experimentally characterized PUPs and their homologs in human gut microbiome. This work also performed a systematic classification of PUPs into enzyme classes, families, and subfamilies. The signature Pfam domains were identified for PUP families, enabling conserved domain-based PUP annotation. This standardized sequence similarity-based PUP classification system offered a guideline for the future inclusion of new experimentally characterized PUPs and the creation of new PUP families. An in-depth data analysis was further conducted on PUP homologs and physically linked PUP gene clusters (PGCs) in gut microbiomes of different human populations.

show abstract

“…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 .…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2022

View full text Add to dashboard Cite

White-fleshed pitaya (Selenicereus undatus) and red-fleshed pitaya (Selenicereus costaricensis) are becoming increasingly popular because of their nutritional and medicinal benefits. However, in addition to their beneficial properties, allergy to pitaya fruits has occurred in daily life. In this study, we investigated the protein profile of pitaya fruit seeds and focused on the most reactive proteins against immunoglobulin E (IgE) in sera from allergic patients by immunoblotting. A protein band of approximately 20 kDa displayed a clear reaction with the serum IgE. The protein bands of interest were excised, in-gel digested, and analyzed using liquid chromatography–tandem mass spectrometry (LC–MS/MS), followed by data searching against a restricted database (Caryophyllales in UniProtKB) for protein identification. Immunoinformatic tools were used to predict protein allergenicity. The potential allergens included cupin_1 and heat shock protein 70 (HSP70) in white-fleshed pitaya seeds, and cupin_1, heat shock protein 70, and heat shock protein sti1-like in red-fleshed pitaya seeds are potential allergens. The expression of potential allergens was further verified at the transcriptional level in the species of S. undatus and S. costaricensis.

show abstract

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

Cited by 36 publications

References 107 publications

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

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

Polyphenol Utilization Proteins in the Human Gut Microbiome

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

Contact Info

Product

Resources

About