Chromosome-level genome assembly of Myristica yunnanensis sheds light on genomic limitations underlying its critically endangered status in China

doi:10.1016/j.pld.2025.08.004

Plant Diversity ›› 2025, Vol. 47 ›› Issue (05): 843-847.DOI: 10.1016/j.pld.2025.08.004

• Case Reports • 上一篇

Chromosome-level genome assembly of Myristica yunnanensis sheds light on genomic limitations underlying its critically endangered status in China

Yongting Zhang^a, Zihe Li^a, Xue Liu^a, Peng Zeng^a, Chuan Peng^b,c, Botong Zhou^a, Yingmei Peng^a, Wenbo Zhu^a, Jian Huang^b, Jing Cai^a

a. School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, China;
b. Yunnan Key Laboratory of Forest Ecosystem Stability and Global Change, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;
c. College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China

收稿日期:2025-06-26 修回日期:2025-08-08 出版日期:2025-09-29 发布日期:2025-09-29
通讯作者: Jing Cai,E-mail:jingcai@nwpu.edu.cn
基金资助:
This work was supported by the National Key R&D Program of China (2022YFC3400300).

Chromosome-level genome assembly of Myristica yunnanensis sheds light on genomic limitations underlying its critically endangered status in China

Yongting Zhang^a, Zihe Li^a, Xue Liu^a, Peng Zeng^a, Chuan Peng^b,c, Botong Zhou^a, Yingmei Peng^a, Wenbo Zhu^a, Jian Huang^b, Jing Cai^a

a. School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, China;
b. Yunnan Key Laboratory of Forest Ecosystem Stability and Global Change, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;
c. College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China

Received:2025-06-26 Revised:2025-08-08 Online:2025-09-29 Published:2025-09-29
Contact: Jing Cai,E-mail:jingcai@nwpu.edu.cn
Supported by:
This work was supported by the National Key R&D Program of China (2022YFC3400300).

摘要/Abstract

关键词: Myristica yunnanensis, Critically endangered, Demographic history, Deleterious variants, Conservation strategy

Key words: Myristica yunnanensis, Critically endangered, Demographic history, Deleterious variants, Conservation strategy

Yongting Zhang, Zihe Li, Xue Liu, Peng Zeng, Chuan Peng, Botong Zhou, Yingmei Peng, Wenbo Zhu, Jian Huang, Jing Cai. Chromosome-level genome assembly of Myristica yunnanensis sheds light on genomic limitations underlying its critically endangered status in China[J]. Plant Diversity, 2025, 47(05): 843-847.

参考文献

Agrawal, A.F., Whitlock, M.C., 2012. Mutation load: The fitness of individuals in populations where deleterious alleles are abundant. Annu. Rev. Ecol. Evol. Syst. 43, 115-135.
Burke, K.D., Williams, J.W., Chandler, M.A., et al., 2018. Pliocene and Eocene provide best analogs for near- future climates. Proc. Natl. Acad. Sci. U.S.A. 115, 13288-13293.
Chaw, S.M., Liu, Y.C., Wu, Y.W., et al., 2019. Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. Nat. Plants 5, 63-73.
Chen, J., Hao, Z., Guang, X., et al., 2019. Liriodendron genome sheds light on angiosperm phylogeny and species-pair differentiation. Nat. Plants 5, 18-25.
Clark, P.U., Dyke, A.S., Shakun, J.D., et al., 2009. The Last Glacial Maximum. Science 325, 710-714.
Coleman, A.D., Maroschek, J., Raasch, L., et al., 2021. The Arabidopsis leucine-rich repeat receptor-like kinase MIK2 is a crucial component of early immune responses to a fungal-derived elicitor. New Phytol. 229, 3453-3466.
Dong, S., Liu, M., Liu, Y., et al., 2021. The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids. Hortic. Res. 8, 38.
Dussex, N., Morales, H.E., Grossen, C., et al., 2023. Purging and accumulation of genetic load in conservation. Trends Ecol. Evol. 38, 961-969.
Fu, L., 1992. China Plant Red Data Book-Rare and Endangered Plants, Vol. 1. Science Press, Beijing, pp. 372-373.
Gentry, A.H., 1982. Patterns of neotropical plant species diversity. Evol. Biol. 1-84.
Grossen, C., Ramakrishnan, U., 2024. Genetic load. Curr. Biol. 34, R1216-R1220.
Hanada, K., Zou, C., Lehti-Shiu, M.D., et al., 2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148.
Hoang Van Sam, 2008. Nghien cứu bổ sung một loai Dậu khấu mới thuộc chi Myristica Gronov. cho hệ thực vật Việt Nam (A Species of Myristica Gronov. (Myristicaceae) A new record for flora of Vietnam). Journal KHLN (in Vietnamese).
Holbourn, A.E., Kuhnt, W., Clemens, S.C., et al., 2018. Late Miocene climate cooling and intensification of southeast Asian winter monsoon. Nat. Commun. 9, 1584.
Hu, L., Xu, Z., Wang, M., et al., 2019. The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis. Nat. Commun. 10, 4702.
Humphreys, A.M., Govaerts, R., Ficinski, S.Z., et al., 2019. Global dataset shows geography and life form predict modern plant extinction and rediscovery. Nat. Ecol. Evol. 3, 1043-1047.
IUCN. 2024. The IUCN Red List of Threatened Species. Version 2024-2. https://www.iucnredlist.org/statistics. Accessed on 15 January 2025.
Lex E. F., Jonathan F. W. 2009. Gene duplication and evolutionary novelty in plants. New Phytol.183, 557-564.
Li, J., Ding, Y., 2001. Studies on the chemical constituents from Myristica yunnanensis Y. H. Li. China J. Chin. Materia Medica. 26, 479-481.
Li, Y., 1976. A new species of Myristica from China. Acta Phytotaxon. Sinica. 14, 94-96.
Liu, X., Zhang, W., Zhang, Y., et al., 2024. Chromosome-scale genomes of Quercus sichourensis and Quercus rex provide insights into the evolution and adaptation of Fagaceae. J. Genet. Genomics 51, 554-565.
Ma, C., Dai, J., Xiao, Z., et al., 2017. Community structure and distribution of minimum population species of Myristica yunnanensis. Guihaia 37, 783-790.
Ma, Y., Liu, D., Wariss, H.M., et al., 2022. Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple. Mol. Ecol. 31, 767-779.
Mao, C.L., Zhang, F.L., Yang, T., et al., 2019. The complete chloroplast genome sequence of Myristica yunnanensis (Myristicaceae). Mitochondrial DNA B Resour. 4, 1871-1872.
Nielsen, R., 2005. Molecular signatures of natural selection. Annu. Rev. Genet. 39, 197-218.
Pitman, N.C.A., Terborgh, J.W., Silman, M.R., et al., 2001. Dominance and distribution of tree species in upper Amazonian terra firme forests. Ecology 82, 2101-2117.
Qin, L., Hu, Y., Wang, J., et al., 2021. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. Nat. Plants 7, 1239-1253.
Schaper, E., Anisimova, M., 2015. The evolution and function of protein tandem repeats in plants. New Phytol. 206, 397-410.
Sun, W. B., 2021. List of Yunnan Protected Plant Species with Extremely Small Population (2021). China: Yunnan Science and Technology Press CO., LTD.
Tajima, F., 1989. Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics 123, 585.
Tao, T., Milne, R.I., Li, J., et al., 2024. Conservation genomic investigation of an endangered conifer, Thuja sutchuenensis, reveals low genetic diversity but also low genetic load. Plant Divers. 46, 78-90.
Theissinger, K., Fernandes, C., Formenti, G., et al., 2023. How genomics can help biodiversity conservation. Trends Genet. 39, 545-559.
Thuiller, W., Lavorel, S., Araujo, M.B., et al., 2005. Climate change threats to plant diversity in Europe. Proc. Natl. Acad. Sci. U.S.A. 102, 8245-8250.
Valencia, R., Foster, R.B., Villa, G., et al., 2004. Tree species distributions and local habitat variation in the Amazon: Large forest plot in eastern Ecuador. J. Ecol. 92, 214-229.
Van der Does, D., Boutrot, F., Engelsdorf, T., et al., 2017. The Arabidopsis leucine-rich repeat receptor kinase MIK2/LRR-KISS connects cell wall integrity sensing, root growth and response to abiotic and biotic stresses. PLoS Genetics 13, e1006832.
World Conservation Monitoring Centre, 1998. Myristica yunnanensis. IUCN Red List of Threatened Species. https://doi.org/10.2305/IUCN.UK.1998.RLTS.T32430A9706368.EN.
Xu, L., Chen, X., Zhao, Y., et al., 2017a. Structure Characteristics of Myristica yunnanensis Community in Xishuangbanna of Yunnan. J. Fujian For. Sci. Tech. 44, 100-112.
Xu, L., Tan, S., Zhao, Y., et al., 2017b. Population structure and Dynamics of Myristicaceae yunnanensis in Xishuangbanna of Yunnan. J. Sichuan For. Sci. Tech. 38, 11-15.
Yang, Y., Ma, T., Wang, Z., et al., 2018. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat. Commun. 9, 5449.
Yang, Z., Liang, L., Xiang, W., et al., 2024. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis. Plant Divers. 46, 294-308.
Yin, Y., Peng, F., Zhou, L., et al., 2021. The chromosome-scale genome of Magnolia officinalis provides insight into the evolutionary position of Magnoliids. iScience 24, 102997.
Zhang, F., Li, X., Mao, C., et al., 2019. Morphological variations and fatty acid composition of seed from wild Myristica yunnanensis Y. H. Li. China Oils Fats 44, 76-80.
Zhang, L., Chen, Fei, Zhang, X., et al., 2020. The water lily genome and the early evolution of flowering plants. Nature 577, 79-84.
Zheng, Y., Yang, D., Yin, X., et al., 2024. The chromosome-level genome assembly of Cananga odorata provides insights into its evolution and terpenoid biosynthesis. New Phytol. 243, 2279-2294.

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Chromosome-level genome assembly of Myristica yunnanensis sheds light on genomic limitations underlying its critically endangered status in China

Chromosome-level genome assembly of Myristica yunnanensis sheds light on genomic limitations underlying its critically endangered status in China

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