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Article|01 Jan 2021|OPEN
Genome and transcriptome of Papaver somniferum Chinese landrace CHM indicates that massive genome expansion contributes to high benzylisoquinoline alkaloid biosynthesis
Li Pei1, Baishi Wang1,2, Jian Ye1, Xiaodi Hu3, Lihong Fu2, Kui Li3, Zhiyu Ni2,4, Zhenlong Wang5, Yujie Wei6, Luye Shi5, Ying Zhang1, Xue Bai1, Mengwan Jiang5, Shuhui Wang7, Chunling Ma2, Shujin Li2, Kaihui Liu1, Wanshui Li1 & Bin Cong2,
1Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, 100038, Beijing, People’s Republic of China
2College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Innovation Center of Forensic Medical Molecular Identification, No. 361 Zhongshan East Road, 050017, Shijiazhuang, Hebei, People’s Republic of China
3Novogene Bioinformatics Institute, Beijing, People’s Republic of China
4Hebei University, No. 180 Wusidong Road, Baoding, Hebei Province, People’s Republic of China
5School of Life Sciences, Zhengzhou University, No. 100 Science Road, 450001, Zhengzhou, Henan, People’s Republic of China
6Gansu Academy of Agri-Engineering Technology, No. 234 Xinzhen Road, Huangyang Town, Liangzhou District, 733006, Wuwei, Gansu, People’s Republic of China
7Wuhan Botanical Garden, Chinese Academy of Sciences, 430074, Wuhan, People’s Republic of China

Horticulture Research 8,
Article number: 5 (2021)
doi: 10.1038/hortres.2021.5
Views: 420

Received: 22 Jun 2020
Revised: 10 Sep 2020
Accepted: 22 Oct 2020
Published online: 01 Jan 2021

Abstract

Opium poppy (Papaver somniferum) is a source of morphine, codeine, and semisynthetic derivatives, including oxycodone and naltrexone. Here, we report the de novo assembly and genomic analysis of P. somniferum traditional landrace ‘Chinese Herbal Medicine’. Variations between the 2.62 Gb CHM genome and that of the previously sequenced high noscapine 1 (HN1) variety were also explored. Among 79,668 protein-coding genes, we functionally annotated 88.9%, compared to 68.8% reported in the HN1 genome. Gene family and 4DTv comparative analyses with three other Papaveraceae species revealed that opium poppy underwent two whole-genome duplication (WGD) events. The first of these, in ancestral Ranunculales, expanded gene families related to characteristic secondary metabolite production and disease resistance. The more recent species-specific WGD mediated by transposable elements resulted in massive genome expansion. Genes carrying structural variations and large-effect variants associated with agronomically different phenotypes between CHM and HN1 that were identified through our transcriptomic comparison of multiple organs and developmental stages can enable the development of new varieties. These genomic and transcriptomic analyses will provide a valuable resource that informs future basic and agricultural studies of the opium poppy.