4.7 Article

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

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HORTICULTURE RESEARCH
卷 8, 期 1, 页码 -

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OXFORD UNIV PRESS INC
DOI: 10.1038/s41438-020-00455-1

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  1. Central Public-interest Scientific Institution Basal Research Fund for the Chinese Academy of Tropical Agricultural Sciences [1630092020003, 1630052019022]
  2. Integrated Demonstration of Key Techniques for the Industrial Development of Featured Crops in Rocky Desertification Areas of Yunnan-Guangxi-Guizhou Provinces [SMH2019-2021]
  3. Foundation of the State Key Laboratory of Biobased Material and Green Papermaking [23190444]

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This study presents a chromosome-scale genome assembly of passion fruit, with insights into genome evolution, gene families, and metabolic pathways involved in the synthesis of important volatile organic compounds. The research identifies key genes and pathways contributing to passion fruit flavor traits, providing valuable resources for improved cultivation practices.
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 similar to 1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91% (similar to 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.

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