猴面包树染色体水平基因组揭示其进化轨迹和环境适应-动脉网

Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation

Nature 等信源发布 2024-10-12 22:08

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AbstractBaobab (Adansonia digitata) is a long-lived tree endemic to Africa with economic, ecological, and cultural importance, yet its genomic features are underexplored. Here, we report a chromosome-level reference genome anchored to 42 chromosomes for A. digitata, alongside draft assemblies for a sibling tree, two trees from distinct locations in Africa, and A.

。在这里，我们报告了一个染色体水平的参考基因组，该基因组锚定在a.digitata的42条染色体上，以及一棵同胞树，两棵来自非洲不同地点的树和a的草图组件。

za from Madagascar. The baobab genome is uniquely rich in DNA transposons, which make up 33%, while LTR retrotransposons account for 10%. A. digitata experienced whole genome multiplication (WGM) around 30 million years ago (MYA), followed by a second WGM event 3–11 MYA, likely linked to autotetraploidy.

来自马达加斯加的za。猴面包树基因组独特地富含DNA转座子，占33%，而LTR反转录转座子占10%。A、大约3000万年前（MYA），digitata经历了全基因组增殖（WGM），随后发生了第二次WGM事件3-11 MYA，可能与同源四倍体有关。

Resequencing of 25 trees identify three subpopulations, with gene flow across West Africa distinct from East Africa. Gene enrichment and fixation index (Fst) analyses show baobab retained multiple circadian, flowering, and light-responsive genes, which likely support longevity through the UV RESISTANCE LOCUS 8 (UVR8) pathway.

对25棵树的重新测序确定了三个亚群，西非的基因流不同于东非。基因富集和固定指数（Fst）分析表明，猴面包树保留了多个昼夜节律，开花和光响应基因，这些基因可能通过紫外线抗性基因座8（UVR8）途径支持寿命。

In sum, we provide genomic resources and insights for baobab breeding and conservation..

总之，我们为猴面包树的育种和保护提供了基因组资源和见解。。

IntroductionThe African baobab (Adansonia digitata) is a deciduous tree belonging to the Malvaceae family, specifically within the Bombacoideae subfamily. Hereafter, it will be simply referred to as “baobab” with other species like the Australian or Malagasy baobab mentioned as needed in the text. One of the earliest references to baobab was made by Ibn Batuta in the 14th century, who described it as a food and a large, long-living tree in Africa1,2.

简介非洲猴面包树（Adansonia digitata）是属于锦葵科的落叶树，特别是在Bombacoideae亚科中。此后，它将被简单地称为“猴面包树”，文中根据需要提到其他物种，如澳大利亚或马达加斯加猴面包树。14世纪，伊本·巴图塔（IbnBatuta）最早提到了猴面包树，他将其描述为非洲的一种食物和一种大型长寿树1,2。

Colloquially, the baobab is referred to as the ‘upside down tree’ since when it loses its leaves, the branches look like roots; in addition, due to the Hollywood blockbuster “The Lion King”, baobab is also referred to as the “Tree of Life”.Baobab offers various edible parts, i.e., seeds, leaves, roots, flowers, and powdery fruit pulp.

通俗地说，猴面包树被称为“倒立树”，因为当它失去叶子时，树枝看起来像根；此外，由于好莱坞大片《狮子王》，猴面包树也被称为“生命之树”。猴面包提供各种可食用部分，即种子，叶子，根，花和粉状果肉。

The fruit is particularly rich in vitamin C, antioxidants, anti-inflammatory compounds, minerals, and fiber. Beyond its dietary benefits, the bark is used in crafting robes and mats, adding to the economic importance of the baobab tree. Furthermore, the seeds yield oil used in cosmetics3. Baobab seeds contain phytic acids, just like legume seeds; however, proper processing can reduce these acids4.

这种水果特别富含维生素C、抗氧化剂、抗炎化合物、矿物质和纤维。除了对饮食有益外，树皮还用于制作长袍和垫子，增加了猴面包树的经济重要性。此外，种子产生用于化妆品的油3。猴面包树种子含有植酸，就像豆类种子一样；然而，正确的处理可以减少这些酸4。

The recent approval of baobab as a food ingredient by the European Commission and the United States Food and Drug Administration (FDA) has significantly increased demand for baobab products outside of Africa. The estimated value of baobab products was US$8.2 billion in 2022 and is anticipated to reach US$12.1 billion by 20305.

欧洲委员会和美国食品和药物管理局（FDA）最近批准将猴面包树作为食品成分，这大大增加了非洲以外地区对猴面包树产品的需求。2022年，猴面包树产品的估计价值为82亿美元，预计到20305年将达到121亿美元。

Thus, there is economic interest and social need for genomic resources to study, preserve, and increase baobab yields6.Baobabs are among the oldest and largest non-clonal organisms, living over 2400 years with canopies exceeding 500 m3 and trunks about 35 meters wide7. Unlike m.

因此，研究，保存和增加猴面包树产量的基因组资源具有经济利益和社会需求6。猴面包树是最古老和最大的非克隆生物之一，生活了2400多年，树冠超过500立方米，树干约35米宽7。与m不同。

Data availability

数据可用性

The genome assemblies and annotations for Ad77271a, Ad77271b, AdOHT, AdKB, and Aza135 are available through the Michael Lab genome portal [https://resources.michael.salk.edu/baobab/index.html], and are also uploaded to CoGe under ID 67790 – 67801. The raw sequencing reads can be accessed via BioProject 1022505.

Ad77271a、Ad77271b、AdOHT、AdKB和Aza135的基因组组装和注释可通过迈克尔实验室基因组门户网站获得[https://resources.michael.salk.edu/baobab/index.html]，并以ID 67790–67801上传到CoGe。。

Source data are provided with this paper and via Figshare [https://doi.org/10.6084/m9.figshare.26039878]115..

本文通过Figshare提供了源数据[https://doi.org/10.6084/m9.figshare.26039878]115。。

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Kitony, J. K. et al. Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation. Figshare, https://doi.org/10.6084/m9.figshare.26039878 (2024).Download referencesAcknowledgementsWe thank members of the Michael Lab for their comments on the genome work and manuscript.

Kitony，J.K.等人。染色体水平的猴面包树基因组阐明了其进化轨迹和环境适应。Figshare公司，https://doi.org/10.6084/m9.figshare.26039878（2024年）。下载参考文献致谢我们感谢迈克尔实验室成员对基因组工作和手稿的评论。

We also thank the genome sequencing team at Monsanto for the initial genome size survey of the Adansonia species funded by the Illumina Greater Good program awarded to T.P.M. Additionally, we are grateful to Mike Winterstein, USDA, GRIN for sending seed and leaf material from A. digitata tree PI77271 for genome sequencing.

我们还感谢孟山都基因组测序团队对Adansonia物种进行了初步的基因组大小调查，该调查由授予T.P.M.的Illumina Greater Good计划资助。此外，我们感谢美国农业部Mike Winterstein，GRIN从A.digitata树PI77271发送种子和叶片材料进行基因组测序。

This work was supported by the Tang Genome Fund to T.P.M., a Global Challenges Research Fund (GCRF), Nottingham Interdisciplinary Research Award, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme [grant number ERC-StG 679056 HOTSPOT], via a grant to L.Y.

这项工作得到了T.P.M.的Tang Genome基金，全球挑战研究基金（GCRF），诺丁汉跨学科研究奖以及欧盟地平线2020研究与创新计划（授权号ERC StG 679056 HOTSPOT）下的欧洲研究理事会（ERC）的支持。

The 25 samples used for resequencing were prepared with financial support from the National Science Foundation award DEB-1354268 to N.K. and field collecting from Diana Mayne, Sarah M. Venter, and Achille E. Assogbadjo. Finally, we are very grateful to David Baum for his constructive suggestions during the writing of the manuscript.Author informationAuthor notesBradley W.

用于重测序的25个样品是在英国国家科学基金会奖DEB-1354268的资助下制备的，并从Diana Mayne，Sarah M.Venter和Achille E.Assogbadjo进行了现场采集。最后，我们非常感谢David Baum在撰写手稿期间提出的建设性建议。作者信息作者注释Bradley W。

AbramsonPresent address: Noblis, Inc., Washington, DC, USASemar PetrusPresent address: Cepheid, Sunnyvale, CA, USAAuthors and AffiliationsPlant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USAJustine K. Kitony, Kelly Colt, Bradley W. Abramson, Nolan T.

Abramson目前的地址：美国华盛顿特区Noblis公司Semar PetrusPresent地址：美国加利福尼亚州桑尼维尔的造父变星作者和附属机构加利福尼亚州拉荷亚索尔克生物研究所分子和细胞生物学实验室，USAJustine K.Kitony，Kelly Colt，Bradley W.Abramson，Nolan T。

Hartwick, Semar Petrus & Todd P. MichaelBiomedical and Clinical Research Centre (BCRC), College of Health and Allied Sciences, University of Cape Co.

哈特威克（Hartwick），塞马尔·佩特鲁斯（SemarPetrus）和托德·P·迈克尔·生物医学与临床研究中心（BCRC），开普大学健康与联合科学学院。

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PubMed Google ScholarContributionsT.P.M. and L.Y. designed the research; J.K.K., T.P.M., K.C., B.W.A., N.T.H., S.P., and N.K. performed research or analyzed data; E.H.E.K. and N.K. contributed materials and/or tools; J.K.K. and T.P.M. wrote the manuscript. All authors revised the manuscript.Corresponding authorCorrespondence to.

PubMed谷歌学术贡献者。P、 M.和L.Y.设计了这项研究；J、 K.K.，T.P.M.，K.C.，B.W.A.，N.T.H.，S.P。和N.K.进行了研究或分析数据；E、 H.E.K.和N.K.提供了材料和/或工具；J、 K.K.和T.P.M.写了手稿。所有作者都修改了手稿。对应作者对应。

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Competing interests

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Nature Communications thanks Bohdan Lojka, Tao Wan, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

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Reprints and permissionsAbout this articleCite this articleKitony, J.K., Colt, K., Abramson, B.W. et al. Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation.

转载和许可本文引用本文Kitony，J.K.，Colt，K.，Abramson，B.W。等人。染色体水平的猴面包树基因组阐明了其进化轨迹和环境适应。

Nat Commun 15, 8833 (2024). https://doi.org/10.1038/s41467-024-53157-wDownload citationReceived: 14 April 2024Accepted: 03 October 2024Published: 12 October 2024DOI: https://doi.org/10.1038/s41467-024-53157-wShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

《国家公社》158833（2024）。https://doi.org/10.1038/s41467-024-53157-wDownload引文收到日期：2024年4月14日接受日期：2024年10月3日发布日期：2024年10月12日OI：https://doi.org/10.1038/s41467-024-53157-wShare本文与您共享以下链接的任何人都可以阅读此内容：获取可共享链接对不起，本文目前没有可共享的链接。复制到剪贴板。

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