Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

被引：67

作者：

Huang, Yue ^{[1
,2
]}

He, Jiaxian ^{[1
]}

Xu, Yuantao ^{[1
,2
]}

Zheng, Weikang ^{[1
]}

Wang, Shaohua ^{[3
]}

Chen, Peng ^{[4
]}

Zeng, Bin ^{[4
]}

Yang, Shuizhi ^{[4
]}

Jiang, Xiaolin ^{[1
]}

Liu, Zishuang ^{[1
]}

Wang, Lun ^{[1
]}

Wang, Xia ^{[1
]}

Liu, Shengjun ^{[1
]}

Lu, Zhihao ^{[1
]}

Liu, Ziang ^{[1
]}

Yu, Huiwen ^{[1
]}

Yue, Jianqiang ^{[3
]}

Gao, Junyan ^{[3
]}

Zhou, Xianyan ^{[3
]}

Long, Chunrui ^{[3
]}

Zeng, Xiuli ^{[5
]}

Guo, Yong-Jie ^{[6
,7
]}

Zhang, Wen-Fu ^{[8
]}

Xie, Zongzhou ^{[1
]}

Li, Chunlong ^{[1
]}

Ma, Zhaocheng ^{[1
]}

Jiao, Wenbiao ^{[1
]}

Zhang, Fei ^{[1
]}

Larkin, Robert M. ^{[1
]}

Krueger, Robert R. ^{[9
]}

Smith, Malcolm W. ^{[10
]}

Ming, Ray ^{[11
]}

Deng, Xiuxin ^{[1
]}

Xu, Qiang ^{[1
,2
]}

机构：

[1] Huazhong Agr Univ, Natl Key Lab Germplasm Innovat Utilizat Hort Crop, Wuhan, Peoples R China

[2] Hubei Hongshan Lab, Wuhan, Peoples R China

[3] Yunnan Acad Agr Sci, Inst Trop & Subtrop Cash Crops, Guizhou, Yunnan, Peoples R China

[4] Hunan Acad Agr Sci, Inst Hort, Changsha, Peoples R China

[5] Minist Agr & Rural Affairs, Qinghai Tibet Plateau Fruit Trees Sci Observat Te, Lhasa, Peoples R China

[6] Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China

[7] Univ Chinese Acad Sci, Beijing, Peoples R China

[8] Chinese Acad Sci, Key Lab Trop Forest Ecol, Xishuangbanna Trop Bot Garden, Mengla, Peoples R China

[9] USDA ARS, Natl Clonal Germplasm Reposit Citrus & Dates, Riverside, CA USA

[10] Department Agr & Fisheries, Bundaberg, Qld, Australia

[11] Univ Illinois, Dept Plant Biol, Urbana, IL USA

来源：

NATURE GENETICS | 2023年 / 55卷 / 11期

基金：

中国国家自然科学基金;

关键词：

PHYLOGENETIC ANALYSIS; VACUOLAR PH; GENOME; RUTACEAE; ACCURATE; ORIGIN; TOOL; CLASSIFICATION; PROGRAM; RETROTRANSPOSONS;

D O I：

10.1038/s41588-023-01516-6

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide, such as sweet orange and lemon. The origin of Citrus species has long been debated and less is known about the Aurantioideae. Here, we compiled the genome sequences of 314 accessions, de novo assembled the genomes of 12 species and constructed a graph-based pangenome for Aurantioideae. Our analysis indicates that the ancient Indian Plate is the ancestral area for Citrus-related genera and that South Central China is the primary center of origin of the Citrus genus. We found substantial variations in the sequence and expression of the PH4 gene in Citrus relative to Citrus-related genera. Gene editing and biochemical experiments demonstrate a central role for PH4 in the accumulation of citric acid in citrus fruits. This study provides insights into the origin and evolution of the orange subfamily and a regulatory mechanism underpinning the evolution of fruit taste.

引用

页码：1964 / 1975

页数：22

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