Chromosome-level genome assembly of Amomum tsao-ko provides insights into the biosynthesis of flavor compounds
Ping Li1,† , Genxiang Bai1,† , Jiangbin He2,† , Bo Liu3,† , Junru Long1,† , Taylan Morcol4 , Weiyao Peng1 , Fan Quan1 , Xinbo Luan1 , Zhenzhen Wang1 , Yi Zhao4 , Yunsheng Cha2 , Yuanyuan Liu5 , Juncai He2 , Lianzhang Wu2 , Yi Yang2 , Edward J. Kennelly4 , Quan Yang6, , Lirong Sun7, , Zepeng Chen8 , Wanqiang Qian3, , Jian Hu2,5, , Jian Yan,1,
1Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, Guangdong Engineering Research Centre for Modern Eco-Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China 2Nujiang Green Spice Industry Research Institute, Lushui, Yunnan, 673100, China 3Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China 4Department of Biological Sciences, Lehman College and The Graduate Center, City University of New York, Bronx, New York, 10468, USA 5Key lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs ,Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China 6School of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou, 510006, China 7State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China 8Guangdong Provincial Tobacco Shaoguan Co. Ltd, Shaoguan, Guangdong, 512000, China *Corresponding author. E-mail: yangquan7208@vip.163.com,slr0807@smu.edu.cn,qianwanqiang@caas.cn,hujian712@gmail.com,yanjian78@scau.edu.cn †Ping Li,Genxiang Bai,Jiangbin He,Bo Liu and Junru Long contributed equally to the study.
Received: 02 Jun 2022 Accepted: 14 Sep 2022 Published online: 19 Sep 2022
Abstract
Amomum tsao-ko is an economically important spice plant in the ginger family (Zingiberaceae). The dried ripe fruit has been widely used as spice and medicine in Southeast Asia due to its distinct flavor metabolites. However, there is little genomic information available to understand the biosynthesis of its characteristic flavor compounds. Here, we present a high-quality chromosome-level genome of A. tsao-ko with a total length of 2.08 Gb assembled into 24 chromosomes. Potential relationships between genetic variation and chemical constituents were analyzed by a genome-wide association study of 119 representative A. tsao-ko specimens in China. Metabolome and transcriptome correlation analysis of different plant organs and fruit developmental stages revealed the proposed biosynthesis of the characteristic bicyclononane aldehydes and aromatic metabolites in A. tsao-ko fruit. Transcription factors of 20 families may be involved in the regulatory network of terpenoids. This study provides genomic and chemical insights into the biosynthesis of characteristic aroma and flavor constituents, which can be used to improve the quality of A. tsao-ko as food and medicine.
, Lirong Sun7 ,
