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Pei L, Wang B, Ye J, Hu X, Fu L, Li K, Ni Z, Wang Z, Wei Y, Shi L, Zhang Y, Bai X, Jiang M, Wang S, Ma C, Li S, Liu K, Li W, Cong B. Genome and transcriptome of Papaver somniferum Chinese landrace CHM indicates that massive genome expansion contributes to high benzylisoquinoline alkaloid biosynthesis. HORTICULTURE RESEARCH 2021; 8:5. [PMID: 33384435 PMCID: PMC7775465 DOI: 10.1038/s41438-020-00435-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/10/2020] [Accepted: 10/22/2020] [Indexed: 05/09/2023]
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.
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Affiliation(s)
- Li Pei
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, 100038, Beijing, People's Republic of China
| | - Baishi Wang
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, 100038, Beijing, People's Republic of China
- College 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
| | - Jian Ye
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, 100038, Beijing, People's Republic of China
| | - Xiaodi Hu
- Novogene Bioinformatics Institute, Beijing, People's Republic of China
| | - Lihong Fu
- College 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
| | - Kui Li
- Novogene Bioinformatics Institute, Beijing, People's Republic of China
| | - Zhiyu Ni
- College 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
- Hebei University, No. 180 Wusidong Road, Baoding, Hebei Province, People's Republic of China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, No. 100 Science Road, 450001, Zhengzhou, Henan, People's Republic of China
| | - Yujie Wei
- Gansu Academy of Agri-Engineering Technology, No. 234 Xinzhen Road, Huangyang Town, Liangzhou District, 733006, Wuwei, Gansu, People's Republic of China
| | - Luye Shi
- School of Life Sciences, Zhengzhou University, No. 100 Science Road, 450001, Zhengzhou, Henan, People's Republic of China
| | - Ying Zhang
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, 100038, Beijing, People's Republic of China
| | - Xue Bai
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, 100038, Beijing, People's Republic of China
| | - Mengwan Jiang
- School of Life Sciences, Zhengzhou University, No. 100 Science Road, 450001, Zhengzhou, Henan, People's Republic of China
| | - Shuhui Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, 430074, Wuhan, People's Republic of China
| | - Chunling Ma
- College 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
| | - Shujin Li
- College 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
| | - Kaihui Liu
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, 100038, Beijing, People's Republic of China
| | - Wanshui Li
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, 100038, Beijing, People's Republic of China
| | - Bin Cong
- College 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.
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Knutsen HK, Alexander J, Barregård L, Bignami M, Brüschweiler B, Ceccatelli S, Cottrill B, Dinovi M, Edler L, Grasl-Kraupp B, Hogstrand C, Hoogenboom LR, Nebbia CS, Oswald IP, Petersen A, Rose M, Roudot AC, Schwerdtle T, Vollmer G, Wallace H, Benford D, Calò G, Dahan A, Dusemund B, Mulder P, Németh-Zámboriné É, Arcella D, Baert K, Cascio C, Levorato S, Schutte M, Vleminckx C. Update of the Scientific Opinion on opium alkaloids in poppy seeds. EFSA J 2018; 16:e05243. [PMID: 32625895 PMCID: PMC7009406 DOI: 10.2903/j.efsa.2018.5243] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Poppy seeds are obtained from the opium poppy (Papaver somniferum L.). They are used as food and to produce edible oil. The opium poppy plant contains narcotic alkaloids such as morphine and codeine. Poppy seeds do not contain the opium alkaloids, but can become contaminated with alkaloids as a result of pest damage and during harvesting. The European Commission asked EFSA to provide an update of the Scientific Opinion on opium alkaloids in poppy seeds. The assessment is based on data on morphine, codeine, thebaine, oripavine, noscapine and papaverine in poppy seed samples. The CONTAM Panel confirms the acute reference dose (ARfD) of 10 μg morphine/kg body weight (bw) and concluded that the concentration of codeine in the poppy seed samples should be taken into account by converting codeine to morphine equivalents, using a factor of 0.2. The ARfD is therefore a group ARfD for morphine and codeine, expressed in morphine equivalents. Mean and high levels of dietary exposure to morphine equivalents from poppy seeds considered to have high levels of opium alkaloids (i.e. poppy seeds from varieties primarily grown for pharmaceutical use) exceed the ARfD in most age groups. For poppy seeds considered to have relatively low concentrations of opium alkaloids (i.e. primarily varieties for food use), some exceedance of the ARfD is also seen at high levels of dietary exposure in most surveys. For noscapine and papaverine, the available data do not allow making a hazard characterisation. However, comparison of the dietary exposure to the recommended therapeutical doses does not suggest a health concern for these alkaloids. For thebaine and oripavine, no risk characterisation was done due to insufficient data. However, for thebaine, limited evidence indicates a higher acute lethality than for morphine and the estimated exposure could present a health risk.
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