The genome evolution and domestication of tropical fruit mango

Peng Wang,Guopeng Zhu,Xiuxu Ye,Sen Wang,Guodi Huang,Aiping Gao,Zhangguang Ni,Yingfeng Luo,Kexuan Tang,Deyong Gong,Meng Yang,Edgar B Cahoon,Ruibang Luo ,Zhiguo Dang,Zhao Zhong ,June Wei ,Jiangtao Gai,Bing Zhang,Songnian Hu,Huarui Chen,Jianfeng Huang,Min Zhu,Qian Li,Beibei Bai,Shizhou Wu ,Huangkai Zhang,Shenghan Gao,Xinyu Tan,Yeyuan Chen

doi:10.1186/s13059-020-01959-8

Abstract

BackgroundMango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis.ResultsWe generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes.ConclusionsAnalysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces.

Highlights

Mango is one of the world’s most important tropical fruits
Our results show that extensive duplications lead to a large number of members in clade III of chalcone synthase (CHS) genes, and, for the highly expressed genes, they tend to be highly expressed in barks and peels rather than in the flesh of all the four varieties we investigated; this is comparable to high accumulation of urushiols in these tissues in mangoes, suggesting their important roles in the biosynthesis of urushiols in mangoes [2, 63, 64]
We estimated that the mango genome underwent an event of whole-genome duplication (WGD) about 33 million years ago

Summary

Introduction

Mango is one of the world’s most important tropical fruits It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Mango is the member of the genus Mangifera in the Anacardiaceae family [4] Within this genus, most, if not all, cultivated mangoes belong to the species Mangifera indica, dozens of other Mangifera species produce edible fruits [5]. Most, if not all, cultivated mangoes belong to the species Mangifera indica, dozens of other Mangifera species produce edible fruits [5] It has a domestication history of over 4000 years within a large area in the Indo-Burmese and Southeast Asia regions but spreads to other parts of the world since the fourteenth century [6, 7]. Considering its long cultivation history and complex genetic backgrounds, it is still largely unknown if there are varieties that can serve as genetic resources different from germplasms currently preserved and produced

Methods

Results

Discussion

Conclusion