@article{d3fa145d3bf24fcab3ed8323653a18af,
title = "Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits",
abstract = "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.",
author = "Yue Huang and Jiaxian He and Yuantao Xu and Weikang Zheng and Shaohua Wang and Peng Chen and Bin Zeng and Shuizhi Yang and Xiaolin Jiang and Zishuang Liu and Lun Wang and Xia Wang and Shengjun Liu and Zhihao Lu and Ziang Liu and Huiwen Yu and Jianqiang Yue and Junyan Gao and Xianyan Zhou and Chunrui Long and Xiuli Zeng and Guo, \{Yong Jie\} and Zhang, \{Wen Fu\} and Zongzhou Xie and Chunlong Li and Zhaocheng Ma and Wenbiao Jiao and Fei Zhang and Larkin, \{Robert M.\} and Krueger, \{Robert R.\} and Smith, \{Malcolm W.\} and Ray Ming and Xiuxin Deng and Qiang Xu",
note = "We thank D. Mabberley from the University of Oxford, for helpful discussions on citrus taxonomy and suggestions on how to improve the paper. We thank T. J. Siebert from Department of Botany and Plant Science, University of California, Riverside, for discussions on citrus-related genera. We also thank M. Sun for the suggestion on how to reconstruct the ancestral distribution analysis; Z.L. Ning and S.H. Zeng from the South China Botanical Garden, Chinese Academy of Sciences; and G.H. Chen from the Bureau of Agriculture and Rural Affairs, Chenzhou for providing the citrus samples. We thank J.L. Ye, D.Y. Guo and L.L. Zhong from the National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University for support on plant growth, metabolics and the bioinformatics platform. This project was supported by the National Key Research and Development Program of China to Q.X. (nos. 2022YFF1003100 and 2018YFD1000101), the National Natural Science Foundation of China to Q.X. (no. 31925034), Major Special Projects and Key R\&D Projects in Yunnan province to Q.X. (no. 202102AE090054), the Foundation of Hubei Hongshan Laboratory to Q.X. (no. 2021hszd016), Key Project of Hubei Provincial Natural Science Foundation to Q.X. (no. 2021CFA017) and the National Postdoctoral Program for Innovative Talents (no. BX20200146) to Y.X. We thank D. Mabberley from the University of Oxford, for helpful discussions on citrus taxonomy and suggestions on how to improve the paper. We thank T. J. Siebert from Department of Botany and Plant Science, University of California, Riverside, for discussions on citrus-related genera. We also thank M. Sun for the suggestion on how to reconstruct the ancestral distribution analysis; Z.L. Ning and S.H. Zeng from the South China Botanical Garden, Chinese Academy of Sciences; and G.H. Chen from the Bureau of Agriculture and Rural Affairs, Chenzhou for providing the citrus samples. We thank J.L. Ye, D.Y. Guo and L.L. Zhong from the National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University for support on plant growth, metabolics and the bioinformatics platform. This project was supported by the National Key Research and Development Program of China to Q.X. (nos. 2022YFF1003100 and 2018YFD1000101), the National Natural Science Foundation of China to Q.X. (no. 31925034), Major Special Projects and Key R\&D Projects in Yunnan province to Q.X. (no. 202102AE090054), the Foundation of Hubei Hongshan Laboratory to Q.X. (no. 2021hszd016), Key Project of Hubei Provincial Natural Science Foundation to Q.X. (no. 2021CFA017) and the National Postdoctoral Program for Innovative Talents (no. BX20200146) to Y.X.",
year = "2023",
month = nov,
doi = "10.1038/s41588-023-01516-6",
language = "English (US)",
volume = "55",
pages = "1964--1975",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Research",
number = "11",
}