黄皮基因组揭示生物碱多样性和甲基转移酶基因家族进化特征

doi:10.1016/j.jia.2024.07.043

Journal of Integrative Agriculture ›› 2024, Vol. 23 ›› Issue (10): 3537-3553.DOI: 10.1016/j.jia.2024.07.043

黄皮基因组揭示生物碱多样性和甲基转移酶基因家族进化特征

收稿日期:2023-07-13 接受日期:2024-04-29 出版日期:2024-10-20 发布日期:2024-09-11

The Clausena lansium genome provides new insights into alkaloid diversity and the evolution of the methyltransferase family

Yongzan Wei^{1, 4, 7*}, Yi Wang^3*, Fuchu Hu^2*, Wei Wang^{1, 7*}, Changbin Wei⁴, Bingqiang Xu⁵, Liqin Liu⁴, Huayang Li³, Can Wang⁶, Hongna Zhang^6#, Zhenchang Liang^3#, Jianghui Xie^{1, 4, 7#}

¹State Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
²Key Laboratory of Genetic Resources Evaluation and Utilization of Tropical Fruits and Vegetables (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou 571100, China
³ Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
⁴Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture and Rural Affairs), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
⁵Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
⁶ Sanya Institute of Breeding and Multiplication/School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
⁷ Sanya Research Academy, Chinese Academy of Tropical Agricultural Sciences, Sanya 572019, China

Received:2023-07-13 Accepted:2024-04-29 Online:2024-10-20 Published:2024-09-11
About author:Yongzan Wei, E-mail: wyz4626@163.com; Yi Wang, E-mail: wangyi19881107@163.com; Fuchu Hu, E-mail: hufuchu@163.com; Wei Wang, E-mail: wangwei@itbb.org.cn; #Correspondence Jianghui Xie, Tel: +86-898-66986419, E-mail: xiejianghui@itbb.org.cn; Zhenchang Liang, Tel: +86-10-62836079, E-mail: zl249@ibcas.ac.cn; Hongna Zhang, Tel: +86-898-66218921, E-mail: 13692476979@139.com * These authors contributed equally to this study.
Supported by:
This work was supported by the Central Public-interest Scientific Institution Basal Research Fund for the Chinese Academy of Tropical Agricultural Sciences (1630062019010 and 1630062020010), and the Fund of Protection of Species Resources for the Ministry of Agriculture and Rural Affairs of China (125A0605).

摘要/Abstract

摘要：

黄皮（Clausena lansium）是一种重要的常绿果树，原产于我国华南地区，其药用价值具有悠久的历史。本研究构建了黄皮（C. lansium）染色体水平基因组，其大小为282.9 Mb，scaffold N50达到30.75 Mb。组装后的基因组包含48.70%的重复元件和24,381个蛋白质编码基因。比较基因组分析表明：黄皮（C. lansium）在约1591 - 2495万年前从柑橘亚科（Aurantioideae）分化而来。在扩张和特有基因中，鉴定出一批与甲基转移酶活性和S-腺苷蛋氨酸依赖性甲基转移酶活性相关的基因。进一步分析表明，N-甲基转移酶（NMT）主要参与生物碱的合成，而O-甲基转移酶（OMT）则参与黄皮香豆素积累的调控，推测黄皮富含生物碱和香豆素的重要原因可能由于NMT和OMT的基因扩张所致，其中串联重复事件是NMT扩展的主要原因。因此，黄皮（C. lansium）参考基因组发布将推动黄皮资源药用化合物发掘及其生物合成通路解析

Abstract:

Wampee (Clausena lansium) is an important evergreen fruit tree native to southern China that has a long history of use for medicinal purposes. Here, a chromosome-level genome of C. lansium was constructed with a genome size of 282.9 Mb and scaffold N50 of 30.75 Mb. The assembled genome contains 48.70% repetitive elements and 24,381 protein-coding genes. Comparative genomic analysis showed that C. lansium diverged from Aurantioideae 15.91–24.95 million years ago. Additionally, some expansive and specific gene families related to methyltransferase activity and S-adenosylmethionine-dependent methyltransferase activity were also identified. Further analysis indicated that N-methyltransferase (NMT) is mainly involved in alkaloid biosynthesis and O-methyltransferase (OMT) participates in the regulation of coumarin accumulation in wampee. This suggested that wampee’s richness in alkaloids and coumarins might be due to the gene expansions of NMT and OMT. The tandem repeat event was one of the major reasons for the NMT expansion. Hence, the reference genome of C. lansium will facilitate the identification of some useful medicinal compounds from wampee resources and reveal their biosynthetic pathways.

Key words: Clausena lansium , genome , evolution , methyltransferase activity , alkaloid biosynthesis , coumarin accumulation

Yongzan Wei, Yi Wang, Fuchu Hu, Wei Wang, Changbin Wei, Bingqiang Xu, Liqin Liu, Huayang Li, Can Wang, Hongna Zhang, Zhenchang Liang, Jianghui Xie. 黄皮基因组揭示生物碱多样性和甲基转移酶基因家族进化特征[J]. Journal of Integrative Agriculture, 2024, 23(10): 3537-3553.

Yongzan Wei, Yi Wang, Fuchu Hu, Wei Wang, Changbin Wei, Bingqiang Xu, Liqin Liu, Huayang Li, Can Wang, Hongna Zhang, Zhenchang Liang, Jianghui Xie. The Clausena lansium genome provides new insights into alkaloid diversity and the evolution of the methyltransferase family[J]. Journal of Integrative Agriculture, 2024, 23(10): 3537-3553.

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黄皮基因组揭示生物碱多样性和甲基转移酶基因家族进化特征

The Clausena lansium genome provides new insights into alkaloid diversity and the evolution of the methyltransferase family

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