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Article|30 Apr 2021|OPEN
The chromosome-level Hemerocallis citrina Borani genome provides new insights into the rutin biosynthesis and the lack of colchicine
Zhixing Qing1,2, Jinghong Liu1, Xinxin Yi3, Xiubin Liu1,4, Guoan Hu5, Jia Lao5, Wei He5, Zihui Yang1, Xiaoyan Zou1,2, Mengshan Sun1, Peng Huang1,4, & Jianguo Zeng1,2,6,
1Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
2 College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
3Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei 430075, China
4College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410125, China
5Green Melody Bio-engineering Group Company Limited, Changsha, Hunan 410329, China
6National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China

Horticulture Research 8,
Article number: 89 (2021)
doi: 10.1038/hortres.2021.89
Views: 407

Received: 03 Sep 2020
Revised: 11 Mar 2021
Accepted: 26 Apr 2021
Published online: 30 Apr 2021

Abstract

Hemerocallis citrina Borani (huang hua cai in Chinese) is an important horticultural crop whose flower buds are widely consumed as a delicious vegetable in Asia. Here we assembled a high-quality reference genome of H. citrina using single-molecule sequencing and Hi-C technologies. The genome assembly was 3.77 Gb and consisted of 3183 contigs with a contig N50 of 2.09 Mb, which were further clustered into 11 pseudochromosomes. A larger portion (3.25 Gb or 86.20%) was annotated as a repetitive content and 54,295 protein-coding genes were annotated in the genome. Genome evolution analysis showed that H. citrina experienced a recent whole-genome duplication (WGD) event at ~15.73 million years ago (Mya), which was the main factor leading to many multiple copies of orthologous genes. We used this reference genome to predict 20 genes involved in the rutin biosynthesis pathway. Moreover, our metabolomics data revealed neither colchicine nor its precursors in H. citrina, challenging the long-standing belief that this alkaloid causes poisoning by the plant. The results of our disruptive research are further substantiated by our genomic finding that H. citrina does not contain any genes involved in colchicine biosynthesis. The high-quality genome lays a solid foundation for genetic research and molecular breeding of H. citrina.