Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims)

Zhiqiang Xia,Meiling Zou,Huanyu Xu,Yi Xu,Xincheng Zhou,Wenquan Wang,Shengkui Zhang,Dongmei Huang,Shun Song,Rulin Zhan,Funing Ma,Bingqiang Xu,Di Chen,Bin Wu

doi:10.1038/s41438-020-00455-1

Abstract

Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that ‘alpha-linolenic acid metabolism’, ‘metabolic pathways’, and ‘secondary metabolic pathways’ were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.

Highlights

Passiflora, which belongs to the Passifloraceae family in the Malpighiales order, includes more than 520 species worldwide, most of which are distributed in the Americas, including Colombia, Brazil, Ecuador, and Peru, with a few in other tropical and subtropical areas, such as southeastAsia, Australia, and New Zealand[1,2]
Duplicate removal, sorting, and quality assessment were performed with high-throughput chromosome conformation capture (Hi-C)-Pro, and uniquely mapped valid reads were used for Hi-C scaffolding (Supplementary Fig. 3)
The differential metabolites were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the results showed that these pathways were mainly enriched in the following: ‘metabolic pathways’, ‘lipoic acid metabolism’, ‘fatty acid biosynthesis’, ‘biosynthesis of secondary metabolites’, and ‘alpha-linolenic acid metabolism’ (Fig. 3e)

Summary

Introduction

Passiflora, which belongs to the Passifloraceae family in the Malpighiales order, includes more than 520 species worldwide, most of which are distributed in the Americas, including Colombia, Brazil, Ecuador, and Peru, with a few in other tropical and subtropical areas, such as southeastAsia, Australia, and New Zealand[1,2]. Passiflora, which belongs to the Passifloraceae family in the Malpighiales order, includes more than 520 species worldwide, most of which are distributed in the Americas, including Colombia, Brazil, Ecuador, and Peru, with a few in other tropical and subtropical areas, such as southeast. Passiflora species are widely cultivated in tropical and subtropical areas of the world due to their edible, Xia et al Horticulture Research (2021)8:14 medicinal, and ornamental value[5,6]. In terms of edible value, Passiflora ranks second in the category of edible fruits, with ~60 fruits, including those from P. edulis, P. edulis f. In terms of medicinal value, many Passiflora plants have a long history of use in traditional folk medicines in some American and European countries[8] as remedies for many neurogenic diseases. The extracts from the leaves, fruits, rind, and seeds have been reported to contain C-glycosyl flavonoids, including vitexin, isovitexin, orientin, isoorientin, luteolin, apigenin, kaempferol, and other active substances with sedative, antioxidant, anti-inflammatory, anxiolytic, and anticarcinogenic effects[9,10,11]

Methods

Results

Conclusion