AbstractAsparagales, the largest monocot order, is renowned for its ecological, economic, and medicinal significance. Here, we leverage transcriptome data from 455 Asparagales species to explore the phylogeny of Asparagales. Moreover, we investigate the evolutionary patterns of the genes involved in allium flavor formation.

摘要天冬酰胺是最大的单子叶植物目，以其生态，经济和药用意义而闻名。在这里，我们利用来自455种天冬酰胺物种的转录组数据来探索天冬酰胺的系统发育。此外，我们研究了参与葱风味形成的基因的进化模式。

We not only establish a robust bifurcating phylogeny of Asparagales but also explore their reticulate relationships. Notably, we find that eight genes involved in the biosynthesis of allium flavor compounds underwent expansion in Allium species. Furthermore, we observe Allium-specific mutations in one amino acid within alliinase and three within lachrymatory factor synthase.

我们不仅建立了天冬酰胺的强大分叉系统发育，而且还探索了它们的网状关系。值得注意的是，我们发现参与葱风味化合物生物合成的八个基因在葱属物种中经历了扩增。此外，我们观察到蒜氨酸酶中一个氨基酸和泪腺因子合酶中三个氨基酸的蒜特异性突变。

Overall, our findings highlight the role of gene expansion, increased expression, and amino acid mutations in driving the evolution of Allium-specific compounds. These insights not only deepen our understanding of the phylogeny of Asparagales but also illuminate the genetic mechanisms underpinning specialized compounds..

总体而言，我们的发现突出了基因扩增，表达增加和氨基酸突变在驱动葱特异性化合物进化中的作用。这些见解不仅加深了我们对天冬酰胺系统发育的理解，而且阐明了支持特殊化合物的遗传机制。。

IntroductionAsparagales consists of approximately 1030 genera and 39,000 species distributed across 14 families, including Orchidaceae, which is one of the largest families of angiosperms according to the Angiosperm Phylogeny Group [APG] IV1 and the Plants of World Online (POWO; https://powo.science.kew.org/).

简介天冬酰胺由大约1030属39000种组成，分布在14个科中，包括兰科，根据被子植物系统发育组（APG）IV1和世界植物在线（POWO）；https://powo.science.kew.org/)。

Known for their diverse applications, Asparagales species serve as vegetables (onions, chives, garlic, asparagus), spices (vanilla), and ornamentals (orchids) and possess medicinal properties (Gastrodiae Rhizoma [Tianma] and Dendrobii Caulis [Shihu] in China and Cypripedium species in North America).

芦笋因其多种应用而闻名，可作为蔬菜（洋葱，韭菜，大蒜，芦笋），香料（香草）和观赏植物（兰花），并具有药用特性（中国的天麻，石斛，北美的鲤属）。

Despite several studies having investigated the phylogeny of Asparagales2,3, there is still uncertainty regarding its evolutionary relationships. One area of debate involves the families Ixioliriaceae, Tecophilaeaceae, and Doryanthaceae. Analyses based only on plastid rbcL supported a relationship (Ixioliriaceae, (Tecophilaeaceae, (Doryanthaceae, others)))4.

尽管有几项研究调查了天冬酰胺2,3的系统发育，但其进化关系仍存在不确定性。争论的一个领域涉及Ixioliriaceae，Tecophilaeae和Doryanthaceae家族。仅基于质体rbcL的分析支持一种关系（Ixioliriaceae，（Tecophilaeae，（Doryanthaceae，其他）））4。

In contrast, analyses using plastid genomes5 and nuclear genes6,7,8 suggested alternative topologies. Transcriptome-based phylogenetics are robust approaches9,10 that can be used to explore the phylogeny of Asparagales better.Asparagales has a global distribution spanning all continents, with North America and Asia exhibiting the highest species diversity, according to POWO.

相反，使用质体基因组5和核基因6,7,8的分析提出了替代拓扑。基于转录组的系统发育学是强有力的方法9,10，可用于更好地探索天冬酰胺的系统发育。据POWO称，天冬酰胺在全球各大洲均有分布，其中北美和亚洲的物种多样性最高。

Several studies investigated the biogeography of Asparagales11,12,13,14. For example, the ancestral area for Asteliaceae11, Blandfordiaceae11, Boryaceae11, Iridaceae13, and Orchidaceae14 was determined to be Australia. In total, biogeographic origins for 11 out of the 14 families within Asparagales are reported to be from Australia, South Africa, or Gondwana.

。例如，Asteliaceae11，Blandfordiaceae11，Boryaceae11，Iridaceae13和Orchidaceae14的祖先区域被确定为澳大利亚。据报道，Asparagales内14个家族中有11个家族的生物地理起源来自澳大利亚，南非或冈瓦纳大陆。

However, the biogeographic origins of the remaining three families, Amaryllidaceae, A.

然而，其余三个科，石蒜科，A的生物地理起源。

We employed ultra-high performance liquid chromatography (UPLC) with quadrupole time-of-flight (QTOF) mass spectrometry (MS) to detect eight compounds in the CSOs biosynthesis pathway across nine Allium species and seven other species within Asparagales. The results indicated that three compounds upstream of the CSOs biosynthesis pathway—serine, valine, and glutathione—were detected in both Allium and non-Allium species (Fig. 3a).

我们采用超高效液相色谱（UPLC）和四极杆飞行时间（QTOF）质谱（MS）检测了9种葱属物种和天冬酰胺中其他7种物种的CSO生物合成途径中的8种化合物。结果表明，在葱属和非葱属物种中均检测到CSO生物合成途径上游的三种化合物-丝氨酸，缬氨酸和谷胱甘肽（图3a）。

However, the remaining five compounds were exclusively detected in Allium species (Fig. 3a and Supplementary Figs. 9 and 10). Refer to Supplementary Data 6 for details about the compounds. Notably, γ-glutamyl-S-allylcysteine emerged as the most upstream metabolite, specific to Allium in the pathway.

然而，其余五种化合物仅在葱属物种中检测到（图3a和补充图9和10）。有关化合物的详细信息，请参阅补充数据6。值得注意的是，γ-谷氨酰-S-烯丙基半胱氨酸是该途径中葱属特有的最上游代谢物。

The gene responsible for synthesizing γ-glutamyl-S-allylcysteine could play a pivotal role in the pathway despite its unreported status.Fig. 3: Identification of S-Alk(en)ylcysteine sulfoxides (CSOs) using UPLC-QTOF-MS.a A summary of metabolites identified for 16 Asparagales species. b Extracted-ion chromatograms of isoalliin and alliin from nine Allium species.

尽管尚未报道，但负责合成γ-谷氨酰-S-烯丙基半胱氨酸的基因可能在该途径中起关键作用。图3：使用UPLC-QTOF-MS鉴定S-Alk（en）基半胱氨酸亚砜（CSO）.a鉴定出16种天冬酰胺物种的代谢物的总结。b从9种葱属植物中提取异蒜氨酸和蒜氨酸的离子色谱图。

Plant photos were taken by Bing Liu, Xiao-Wei Xin, Xiao-Xiao Wang, and Ling-Yun Chen. c Secondary ion fragments for alliin and isoalliin are depicted as shaded areas on the chromatograms. Red numbers indicate the characteristic secondary fragment ion of alliin.Full size imageTwo upstream sub-pathways, designated as way 1 (glutathione biosynthesis) and way 2 (valine catabolism), as illustrated in Fig. 4a, along with a downstream sub-pathway, comprised a total of 13 genes (Supplementary Data 7), involved in CSOs biosynthesis.

植物照片由刘冰、辛晓伟、王晓晓和陈凌云拍摄。c蒜氨酸和异蒜氨酸的二次离子片段被描绘为色谱图上的阴影区域。红色数字表示蒜氨酸的特征性二级碎片离子。全尺寸图像如图4a所示，两个上游子途径，命名为途径1（谷胱甘肽生物合成）和途径2（缬氨酸分解代谢），以及下游子途径，共包含13个基因（补充数据7），参与CSO生物合成。

Gene trees were constructed, and gene copy numbers for each species were quantified (Supplementary Figs. 11–15). The Mann–Whitney U test indicated that three genes in wa.

构建了基因树，并量化了每个物种的基因拷贝数（补充图11-15）。。

Data availability

数据可用性

Raw sequence reads of the 244 samples generated in this study have been deposited in the NCBI Sequence Read Archive under BioProject nos. PRJNA1107703 and PRJNA1107706. Raw reads or annotations for other samples were accessed from the internet with accession nos. provided in Supplementary Data 1. The assembled transcriptomes for the samples sequenced in this study, CDSs and PEPs for all the 501 samples used in phylogenetic analyses, as well as those for the 16 samples used in gene expression level analyses, are available at Figshare: [https://doi.org/10.6084/m9.figshare.25516204].

本研究中产生的244个样品的原始序列读数已保存在生物项目PRJNA1107703和PRJNA1107706下的NCBI序列读取档案中。其他样品的原始读数或注释可从互联网上访问，登录号见补充数据1。本研究中测序的样品的组装转录组，用于系统发育分析的所有501个样品的CDSs和PEPs，以及用于基因表达水平分析的16个样品的转录组，可在Figshare获得：[https://doi.org/10.6084/m9.figshare.25516204]。

Additionally, the sequences of orthologs, data matrices for phylogenetic analyses, divergence times, ancestral area reconstructions, and Source Data are also available at Figshare: [https://doi.org/10.6084/m9.figshare.25516204]. Specimens have been deposited at the Herbarium of Guangxi Botanical Garden of Medicinal Plants..

此外，Figshare还提供了直系同源序列，用于系统发育分析的数据矩阵，发散时间，祖先区域重建和源数据：[https://doi.org/10.6084/m9.figshare.25516204]。标本保存于广西药用植物植物园植物标本室。。

Code availability

代码可用性

Codes used in this study have been deposited at Figshare: [https://doi.org/10.6084/m9.figshare.25516204].

[https://doi.org/10.6084/m9.figshare.25516204]。

ReferencesByng, J. W. et al. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016).Article

参考文献Byng，J。W。等人。开花植物目和科被子植物系统发育组分类的更新：APG IV。Bot。J。Linn。Soc.181，1-20（2016）。文章

Google Scholar

谷歌学者

Zhang, G. et al. Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism. J. Integr. Plant Biol. 65, 1204–1225 (2023).Article

Zhang，G.等人。利用核基因和附生进化见解对兰科进行全面的系统发育分析。J、 整数。植物生物学。651204-1225（2023）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Seberg, O. et al. Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. Am. J. Bot. 99, 875–889 (2012).Article

基于三个质体和两个线粒体基因的天冬酰胺的系统发育。《美国法学杂志》第99875-889页（2012年）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Bremer, K. & Janssen, T. Gondwanan origin of major monocot groups inferred from dispersal-vicariance analysis. Aliso 22, 22–27 (2006).Article

Bremer，K。＆Janssen，T。冈瓦纳主要单子叶植物群的起源，从扩散邻域分析推断。Aliso 22，22–27（2006）。文章

Google Scholar

谷歌学者

Givnish, T. J. et al. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. Am. J. Bot. 105, 1888–1910 (2018).Article

Givnish，T.J.等人，《单子叶植物质体系统发育基因组学》，时间线，物种多样化的净比率，多基因分析的力量以及单子叶植物起源的功能模型。《美国期刊》Bot.1051888-1910（2018）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Timilsena, P. R. et al. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. Front. Plant Sci. 13, 876779 (2022).Article

Timilsena，P.R。等人。使用602个单拷贝核基因和1375个BUSCO基因对顺序和家族水平的单子叶植物关系进行系统基因组解析。正面。植物科学。13876779（2022）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Baker, W. J. et al. A comprehensive phylogenomic platform for exploring the angiosperm tree of life. Syst. Biol. 71, 301–319 (2022).Article

Baker，W.J.等人。探索被子植物生命树的综合系统发育基因组学平台。系统。生物学71301-319（2022）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Zuntini, A. R. et al. Phylogenomics and the rise of the angiosperms. Nature 629, 843–850 (2024).Article

Zuntini，A.R.等人，《系统发育基因组学与被子植物的兴起》。自然629843-850（2024）。文章

ADS

广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Stull, G. W. et al. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. Nat. Plants 7, 1015–1025 (2021).Article

基因重复和系统基因组冲突是裸子植物表型进化的主要脉冲。。文章

PubMed

PubMed

Google Scholar

谷歌学者

Yu, J. et al. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan–Hengduan Mountains. New Phytol. 238, 888–903 (2023).Article

综合系统发育基因组学分析揭示了爬山虎（维生素科）的网状进化，突出了喜马拉雅-横断山脉的物种形成动力学。。238888-903（2023）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Birch, J. L. & Keeley, S. C. Dispersal pathways across the Pacific: the historical biogeography of Astelia s.l. (Asteliaceae, Asparagales). J. Biogeogr. 40, 1914–1927 (2013).Article

Birch，J.L.＆Keeley，S.C.跨越太平洋的扩散途径：Astelia S.L.（Asteliaceae，Asparagales）的历史生物地理学。J、 。401914-1927（2013）。文章

Google Scholar

谷歌学者

Kocyan, A. et al. Molecular phylogenetics of Hypoxidaceae-evidence from plastid DNA data and inferences on morphology and biogeography. Mol. Phylogenet. Evol. 60, 122–136 (2011).Article

。分子系统发育。进化。60122-136（2011）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Goldblatt, P. et al. Iridaceae ‘Out of Australasia’? phylogeny, biogeography, and divergence time based on plastid DNA sequences. Syst. Bot. 33, 495–508 (2008).Article

？基于质体DNA序列的系统发育，生物地理学和发散时间。系统。Bot.33495-508（2008年）。文章

Google Scholar

谷歌学者

Givnish, T. J. et al. Orchid historical biogeography, diversification, Antarctica and the paradox of orchid dispersal. J. Biogeogr. 43, 1905–1916 (2016).Article

Givnish，T.J.等人，《兰花历史生物地理学，多样化，南极洲和兰花扩散的悖论》。J、 。431905-1916（2016）。文章

Google Scholar

谷歌学者

Guo, C. et al. Phylogenomics and the flowering plant tree of life. J. Integr. Plant Biol. 65, 299–323 (2023).Article

郭，C。等。系统发育基因组学和开花植物生命树。J、 整数。植物生物学。65299-323（2023）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Yoshimoto, N. & Saito, K. S-Alk(en)ylcysteine sulfoxides in the genus Allium: proposed biosynthesis, chemical conversion, and bioactivities. J. Exp. Bot. 70, 4123–4137 (2019).Article

吉本，N。＆Saito，K。葱属中的S-烷基半胱氨酸亚砜：拟议的生物合成，化学转化和生物活性。J、 实验Bot 704123-4137（2019）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Liao, N. et al. Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops. Nat. Commun. 13, 6690 (2022).Article

Liao，N。等人。丛生洋葱的染色体水平基因组组装阐明了葱类作物的基因组进化和风味形成。国家公社。。文章

ADS

广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Venâncio, P. C. et al. Antimicrobial activity of two garlic species (Allium sativum and A. tuberosum) against staphylococci infection. In vivo study in rats. Adv. Pharm. Bull. 7, 115–121 (2017).Article

Venáncio，P.C.等人。两种大蒜（大蒜和A.tuberosum）对葡萄球菌感染的抗菌活性。大鼠体内研究。Adv.Pharm.Bull公司。7115-121（2017）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Sun, X. et al. A chromosome-level genome assembly of garlic (Allium sativum) provides insights into genome evolution and allicin biosynthesis. Mol. Plant 13, 1328–1339 (2020).Article

Sun，X。等人。大蒜（Allium sativum）的染色体水平基因组组装提供了对基因组进化和大蒜素生物合成的见解。摩尔工厂11328–1339（2020）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Hao, F. et al. Chromosome-level genomes of three key Allium crops and their trait evolution. Nat. Genet. 55, 1976–1986 (2023).Article

郝，F。等。三种主要葱属作物的染色体水平基因组及其性状进化。纳特·吉内特。551976年至1986年（2023年）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Liu, N. et al. Transcriptome landscapes of multiple tissues highlight the genes involved in the flavor metabolic pathway in Chinese chive (Allium tuberosum). Genomics 113, 2145–2157 (2021).Article

Liu，N.等人。多种组织的转录组景观突出了韭菜（Allium tuberosum）风味代谢途径中涉及的基因。基因组学1132145–2157（2021）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot. 55, 1903–1918 (2004).Article

Jones，M.G.等人，《洋葱和大蒜风味前体的生物合成》。J、 。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Willson, J., Roddur, M. S., Liu, B., Zaharias, P. & Warnow, T. DISCO: species tree inference using multicopy gene family tree decomposition. Syst. Biol. 71, 610–629 (2022).Article

Willson，J.，Roddur，M.S.，Liu，B.，Zaharias，P。＆Warnow，T.DISCO：使用多拷贝基因家族树分解进行物种树推断。系统。生物学71610-629（2022）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinf. 19, 153 (2018).Article

Zhang，C.，Rabiee，M.，Sayyari，E。＆Mirarab，S。ASTRAL-III：从部分解析的基因树重建多项式时间物种树。BMC生物信息。19153（2018）。文章

Google Scholar

谷歌学者

Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).Article

Stamatakis，A。RAxML版本8：用于系统发育分析和大型系统发育后分析的工具。生物信息学301312-1313（2014）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Stevens, P. F. Angiosperm Phylogeny Website. Version 14. http://www.mobot.org/MOBOT/research/APweb/ (2001).Salichos, L., Stamatakis, A. & Rokas, A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol. Evol. 31, 1261–1271 (2014).Article .

Stevens，P.F。被子植物系统发育网站。版本14。http://www.mobot.org/MOBOT/research/APweb/（2001年）。Salichos，L.，Stamatakis，A。＆Rokas，A。基于信息论的新方法，用于量化系统发育树之间的不一致性。分子生物学。进化。311261-1271（2014）。文章。

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Smith, S. A., Moore, M. J., Brown, J. W. & Yang, Y. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evol. Biol. 15, 150 (2015).Article

Smith，S.A.，Moore，M.J.，Brown，J.W。＆Yang，Y。对系统发育基因组数据集的分析揭示了冲突，一致性和基因重复，并以动物和植物为例。BMC进化。。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Pease, J. B., Brown, J. W., Walker, J. F., Hinchliff, C. E. & Smith, S. A. Quartet sampling distinguishes lack of support from conflicting support in the green plant tree of life. Am. J. Bot. 105, 385–403 (2018).Article

Pease，J.B.，Brown，J.W.，Walker，J.F.，Hinchliff，C.E。＆Smith，S.A。四方抽样区分了绿色植物生命树中缺乏支持和相互冲突的支持。《美国期刊》Bot.105385-403（2018）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Wen, D., Yu, Y., Zhu, J. & Nakhleh, L. Inferring phylogenetic networks using PhyloNet. Syst. Biol. 67, 735–740 (2018).Article

Wen，D.，Yu，Y.，Zhu，J。＆Nakhleh，L。使用PhyloNet推断系统发育网络。系统。生物学67735-740（2018）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Rhodes, J. A., Baños, H., Mitchell, J. D. & Allman, E. S. MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R. Bioinformatics 37, 1766–1768 (2021).Article

。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Solís-Lemus, C., Bastide, P. & Ané, C. PhyloNetworks: a package for phylogenetic networks. Mol. Biol. Evol. 34, 3292–3298 (2017).Article

Solís-Lemus，C.，Bastide，P。＆Ané，C。PhyloNetworks：系统发育网络的软件包。分子生物学。进化。343292-3298（2017）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Blair, C. & Ané, C. Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data. Syst. Biol. 69, 593–601 (2020).Article

Blair，C。＆Ané，C。系统发育树和网络可以作为分析基因组数据的强大且互补的方法。系统。生物学69593-601（2020）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Morales-Briones, D. F. et al. Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae s.l. Syst. Biol. 70, 219–235 (2021).Article

Morales-Briones，D.F.等人。解开系统基因组数据集中基因树不一致的来源：测试苋菜科s.l.系统中的古代杂交。生物学70219-235（2021）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Sousa, V. & Hey, J. Understanding the origin of species with genome-scale data: modelling gene flow. Nat. Rev. Genet. 14, 404–414 (2013).Article

Sousa，V。＆Hey，J。用基因组规模的数据了解物种的起源：基因流建模。Genet自然Rev。。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).Article

Bouckaert，R。等人，《野兽2：贝叶斯进化分析的软件平台》。。生物学杂志10，e1003537（2014）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Li, H. T. et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nat. Plants 5, 461–470 (2019).Article

Li，H.T.等人，《被子植物的起源与侏罗纪裂谷之谜》。《自然植物》5461-470（2019）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Pérez-Escobar, O. A. et al. The origin and speciation of orchids. New Phytol. 242, 700–716 (2024).Article

Pérez-Escobar，O.A.等人，《兰花的起源和物种形成》。。242700–716（2024）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Matzke, N. J. BioGeoBEARS: bioGeography with Bayesian (and likelihood) evolutionary analysis with R scripts, version 1.1.1. Zenodo https://doi.org/10.5281/zenodo.1478250 (2018).Wang, Y. et al. Progress in systematics and biogeography of Orchidaceae. Plant Divers. 46, 425–434 (2024).Article .

Matzke，N.J。BioGeoBEARS：使用R脚本进行贝叶斯（和似然）进化分析的生物地理学，版本1.1.1。泽诺多https://doi.org/10.5281/zenodo.1478250（2018年）。Wang，Y。等。兰科植物系统学和生物地理学研究进展。工厂潜水员。46425-434（2024）。文章。

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Markwick, P. J. Paul’s Palaeo Pages. http://www.palaeogeography.net (2011).Chen, D. Y., Zhang, T. K., Chen, Y. M., Ma, H. & Qi, J. Tree2GD: a phylogenomic method to detect large-scale gene duplication events. Bioinformatics 38, 5317–5321 (2022).Article

马克·威克（Markwick，P.J.Paul）的《古书》。http://www.palaeogeography.net。Chen，D.Y.，Zhang，T.K.，Chen，Y.M.，Ma，H.＆Qi，J.Tree2GD：一种检测大规模基因复制事件的系统基因组学方法。生物信息学385317-5321（2022）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Yang, Y. et al. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. New Phytol. 217, 855–870 (2018).Article

Yang，Y。等人改进的转录组取样精确定位了石竹目中26个古老和最近的多倍体事件，包括两个异源多倍体事件。。217855-870（2018）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Qiao, X. et al. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol. 20, 38 (2019).Article

乔，X。等。植物重复多倍体-二倍体循环中的基因复制和进化。基因组生物学。20，38（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Condamine, F. L., Clapham, M. E. & Kergoat, G. J. Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence? Sci. Rep. 6, 19208 (2016).Article

Condamine，F.L.，Clapham，M.E。和Kergoat，G.J。昆虫多样化的全球模式：走向化石和分子证据的调和？科学。代表61928（2016）。文章

ADS

广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Ellis, S. A. & Scatcherd, J. E. Bean seed fly (Delia platura, Delia florilega) and onion fly (Delia antiqua) incidence in England and an evaluation of chemical and biological control options. Ann. Appl. Biol. 151, 259–267 (2007).Article

Ellis，S.A。＆Scatcherd，J.E。豆子蝇（Delia platura，Delia florilega）和洋葱蝇（Delia antiqua）在英格兰的发病率以及化学和生物防治方案的评估。安。应用。生物学151259-267（2007）。文章

Google Scholar

谷歌学者

Ding, S. et al. The phylogeny and evolutionary timescale of Muscoidea (Diptera: Brachycera: Calyptratae) inferred from mitochondrial genomes. PLoS ONE 10, e0134170 (2015).Article

Ding，S.等人。从线粒体基因组推断的蝇科（双翅目：短尾目：有瓣蝇科）的系统发育和进化时间尺度。PLoS ONE 10，e0134170（2015）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Xuan, J. L. et al. The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics. Mol. Phylogenet. Evol. 184, 107778 (2023).Article

Xuan，J.L.等人。锚定系统发育基因组学中采叶蝇（双翅目：潜蝇科）的系统发育和分化时间。分子系统发育。进化。184107778（2023）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Lancaster, J. E. & Boland, M. J. Flavor Biochemistry: Onions and Allied Crops (CRC Press, 1990).Auger, J. et al. Insecticidal and fungicidal potential of Allium substances as biofumigants. Agroindustria 3, 367–370 (2004).Christ, B. et al. Repeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants.

Lancaster，J.E。和Boland，M.J。风味生物化学：洋葱和相关作物（CRC出版社，1990）。Auger，J.等人。葱类物质作为生物增湿剂的杀虫和杀菌潜力。农业产业3367-370（2004）。Christ，B.等人。细胞色素P450介导的植物螺酮甾体生物合成的重复进化。

Nat. Commun. 10, 3206 (2019).Article .

Nat.普通。103206（2019）。文章。

ADS

广告

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Xu, Z. et al. The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales. Plant J. 111, 217–230 (2022).Article

徐，Z。等人。延胡索的基因组揭示了毛茛中苄基异喹啉生物碱生物合成的进化。工厂J.111217–230（2022）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Chen, L. Y. et al. Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments. Mol. Biol. Evol. 39, msac079 (2022).Article

Chen，L.Y。等人。泽泻目的系统基因组学分析揭示了对水生环境的适应。分子生物学。进化。39，msac079（2022）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Beran, F., Kollner, T. G., Gershenzon, J. & Tholl, D. Chemical convergence between plants and insects: biosynthetic origins and functions of common secondary metabolites. New Phytol. 223, 52–67 (2019).Article

Beran，F.，Kollner，T.G.，Gershenzon，J。＆Tholl，D。植物和昆虫之间的化学融合：常见次级代谢产物的生物合成起源和功能。。223,52-67（2019）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Hurni, S. et al. Rye Pm8 and wheat Pm3 are orthologous genes and show evolutionary conservation of resistance function against powdery mildew. Plant J. 76, 957–969 (2013).Article

Hurni，S。等人。黑麦Pm8和小麦Pm3是直系同源基因，显示出对白粉病抗性功能的进化保守性。植物J.76957–969（2013）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Consortium, M. E. G. et al. Phylogenomic mining of the mints reveals multiple mechanisms contributing to the evolution of chemical diversity in Lamiaceae. Mol. Plant 11, 1084–1096 (2018).Article

Consortium，M.E.G.等人。薄荷的系统发育基因组挖掘揭示了多种机制，有助于唇形科化学多样性的进化。摩尔植物111084-1096（2018）。文章

Google Scholar

谷歌学者

Yang, X. et al. Parallel analysis of global garlic gene expression and alliin content following leaf wounding. BMC Plant Biol. 21, 174 (2021).Article

Yang，X。等人。叶片损伤后全球大蒜基因表达和蒜氨酸含量的平行分析。BMC植物生物学。21174（2021）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Yoshimoto, N. et al. Identification of a flavin-containing S-oxygenating monooxygenase involved in alliin biosynthesis in garlic. Plant J. 83, 941–951 (2015).Article

Yoshimoto，N.等人。鉴定大蒜中蒜氨酸生物合成中含有黄素的S-氧合单加氧酶。植物J.83941–951（2015）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Qin, L. et al. Metabolomics and transcriptomics analyses provides insights into S-alk(en)yl cysteine sulfoxides (CSOs) accumulation in onion (Allium cepa). Sci. Hortic. 310, 111727 (2023).Article

秦，L。等人。代谢组学和转录组学分析提供了洋葱（洋葱葱）中S-alk（烯）基半胱氨酸亚砜（CSO）积累的见解。科学。霍特语。310111727（2023）。文章

CAS

中科院

Google Scholar

谷歌学者

Kuettner, E. B., Hilgenfeld, R. & Weiss, M. S. The active principle of garlic at atomic resolution. J. Biol. Chem. 277, 46402–46407 (2002).Article

Kuettner，E.B.，Hilgenfeld，R。＆Weiss，M.S。大蒜在原子分辨率下的活性成分。J、 生物。化学。27746402–46407（2002）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Arakawa, T. et al. Dissecting the stereocontrolled conversion of short-lived sulfenic acid by lachrymatory factor synthase. ACS Catal. 10, 9–19 (2020).Article

Arakawa，T。等。解剖泪腺因子合酶对短寿命亚磺酸的立体控制转化。ACS加泰罗尼亚。10,9-19（2020）。文章

CAS

中科院

Google Scholar

谷歌学者

Song, L. & Florea, L. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. Gigascience 4, 48 (2015).Article

Song，L。＆Florea，L。Rcorrector：Illumina RNA-seq读数的有效且准确的错误校正。Gigascience 4,48（2015）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).Article

Bolger，A.M.，Lohse，M。和Usadel，B。Trimmomatic：用于Illumina序列数据的灵活修剪器。生物信息学302114-2120（2014）。Langmead，B。＆Salzberg，S.L。与Bowtie 2快速间隙读取对齐。《自然方法》9357（2012）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 (2013).Article

Haas，B.J.等人使用Trinity平台从RNA-seq进行从头转录序列重建，以进行参考生成和分析。自然协议。81494-1512（2013）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Haas, B. J. TransDecoder. GitHub https://github.com/TransDecoder/TransDecoder (2016).Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinf. 10, 421 (2009).Article

Haas，B.J。TransDecoder。GitHubhttps://github.com/TransDecoder/TransDecoder（2016年）。Camacho，C。等。BLAST+：体系结构和应用。BMC生物信息。10421（2009）。文章

Google Scholar

谷歌学者

van Dongen, S. M. Graph Clustering by Flow Simulation (University of Utrecht, 2000).Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).Article

van Dongen，S.M。通过流模拟进行图聚类（乌得勒支大学，2000）。Katoh，K。＆Standley，D.M。MAFFT多序列比对软件版本7：性能和可用性的改进。分子生物学。进化。30772-780（2013）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Smith, S. A. & Dunn, C. W. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24, 715–716 (2008).Article

Smith，S.A.＆Dunn，C.W.Phyutility：用于树木，比对和分子数据的系统信息学工具。生物信息学24715-716（2008）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Smith, S. A., Brown, J. W. & Walker, J. F. So many genes, so little time: a practical approach to divergence-time estimation in the genomic era. PLoS ONE 13, e0197433 (2018).Article

Smith，S.A.，Brown，J.W。＆Walker，J.F。如此多的基因，如此少的时间：基因组时代分歧时间估计的实用方法。。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007).Article

Drummond，A.J。和Rambaut，A.BEAST：通过采样树进行贝叶斯进化分析。BMC进化。生物学7214（2007）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Sessa, E. B., Zimmer, E. A. & Givnish, T. J. Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae). Am. J. Bot. 99, 730–750 (2012).Article

Sessa，E.B.，Zimmer，E.A.和Givnish，T.J.系统发育、分化时间和新世界干细胞科的历史生物地理学。Am.J.Bot.99，730-750（2012）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Rognes, T. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinf. 12, 221 (2011).Article

Rognes，T。Faster Smith-Waterman数据库使用序列间SIMD并行化进行搜索。BMC生物信息。12221（2011）。文章

Google Scholar

谷歌学者

Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).Article

Jones，P.等人，《InterProScan 5：基因组规模的蛋白质功能分类》。生物信息学301236-1240（2014）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Huang, C. H. et al. Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Mol. Biol. Evol. 33, 394–412 (2016).Article

Huang，C.H.等人。使用核基因解析芸薹科系统发育揭示了嵌套辐射并支持趋同的形态进化。分子生物学。进化。33394-412（2016）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Smith, S. A. & O’Meara, B. C. TreePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28, 2689–2690 (2012).Article

Smith，S.A。＆O'Meara，B.C。TreePL：使用惩罚可能性对大型系统发育进行发散时间估计。生物信息学282689-2690（2012）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017).Article

Patro，R.，Duggal，G.，Love，M.I.，Irizarry，R.A。＆Kingsford，C.Salmon提供了快速且有偏见的转录本表达定量。自然方法14417-419（2017）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Bailey, T. L., Johnson, J., Grant, C. E. & Noble, W. S. The MEME suite. Nucleic Acids Res. 43, W39–W49 (2015).Article

Bailey，T.L.，Johnson，J.，Grant，C.E.＆Noble，W.S。MEME suite。核酸研究43，W39–W49（2015）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Morris, G. M. et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791 (2009).Article

Morris，G.M.等人。AutoDock4和AutoDockTools4：具有选择性受体灵活性的自动对接。J、 计算机。化学。302785-2791（2009）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A. & Moreno, E. AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4. Biol. Direct 15, 1–12 (2020).Article

Valdés-Tresanco，M.s.，Valdés-Tresanco，M.E.，Valiente，P.A。＆Moreno，E.AMDock：一种多功能的图形工具，用于协助与Autodock Vina和Autodock4进行分子对接。生物学报15，1-12（2020）。文章

Google Scholar

谷歌学者

Laskowski, R. A. & Swindells, M. B. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model. 51, 2778–2786 (2011).Article

Laskowski，R.A。＆Swindells，M.B。LigPlot+：用于药物发现的多配体-蛋白质相互作用图。J、 化学。Inf.模型。512778-2786（2011）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Download referencesAcknowledgementsWe thank the Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Xishuangbanna Tropical Botanical Garden (CAS), Guiyang Medicinal Botanical Garden, and Shenyang Botanical Garden for assistance in plant collection; Can Dai (Hubei University) for discussion on this study; Michael L.

下载参考文献致谢我们感谢中国科学院昆明植物研究所（CAS），西双版纳热带植物园（CAS），贵阳药用植物园和沈阳植物园在植物采集方面的帮助；Can Dai（湖北大学）就这项研究进行了讨论；迈克尔L。

Moody (University of Texas at El Paso) for discussion and providing plant photo; Xu Lu, Hui-Ying Wang (China Pharmaceutical University) and Xiang-Yang Leng (SCIEX, China) for technical assistance; Xiao-Wei Xin (Shandong Drug and Food Vocational College) for providing plant materials; Bing Liu (Institute of Botany, CAS), Zhong Zhang (Jinggangshan National Nature Reserve) and Ye-Chun Xu (Guangdong Academy of Agricultural Sciences) for providing plant photos; Ya-Dong Zhou (Nanchang University) for assisting in data analyses and providing plant photos; Guo-Yong Xie (China Pharmaceutical University) for assisting in plant cultivation; Li Feng, Xing-Ze Li, Wen-Da Zhang, Wen-Fang Zheng, and Wen-Yu Du (China Pharmaceutical University) for assisting in data analyses; John A.

穆迪（德克萨斯大学埃尔帕索分校）进行讨论并提供植物照片；Xu Lu，Hui Ying Wang（中国药科大学）和Xiang Yang Leng（中国SCIEX）提供技术援助；肖伟新（山东医药食品职业学院）提供植物材料；刘冰（中国科学院植物研究所），张忠（井冈山国家级自然保护区）和徐叶春（广东省农业科学院）提供了植物照片；周亚东（南昌大学）协助数据分析并提供植物照片；谢国勇（中国药科大学）协助植物栽培；；约翰·A。

Rhodes (University of Alaska Fairbanks) for explaining the results of MSCquartets; Ji Yang (Fudan University) and Tao Wan (Wuhan Botanical Garden) for suggestions on this manuscript. This work was supported by the Guangxi Innovation-Driven Development Project (no. GuiKe AA18242040 to K.-H.W.), the Construction of Southern Medicine Germplasm Resource Base for Guangdong Northern (20231206 to K.-H.

Rhodes（阿拉斯加州大学费尔班克斯分校）解释了MSCquartets的结果；济阳（复旦大学）和陶湾（武汉植物园）对这份手稿的建议。这项工作得到了广西创新驱动发展项目（桂科AA18242040至K.-H.W.），广东北部南方医学种质资源基地建设（20231206至K.-H.）的支持。

W.), the National Natural Science Foundation of China (32370242 to L.-Y.C.), the Fundamental Research Funds for the Central Universities (2632024TD04 to L.-Y.C.), and the Sino-Africa Joint Research Center (SAJC202101 to Q.-F.W.).Author informationAuthor notesThese authors contri.

W、 ），国家自然科学基金（32370242至洛杉矶），中央大学基础研究基金（2632024TD04至洛杉矶），以及中非联合研究中心（SAJC202101至Q.-F.W.）。作者信息作者注意到这些作者贡献了。

PubMed Google ScholarChien-Hsun HuangView author publicationsYou can also search for this author in

PubMed Google Scholarcien Hsun Huang查看作者出版物您也可以在

PubMed Google ScholarDiego F. Morales-BrionesView author publicationsYou can also search for this author in

PubMed Google ScholarDiego F.Morales BrionesView作者出版物您也可以在

PubMed Google ScholarXiang-Yu WangView author publicationsYou can also search for this author in

PubMed Google ScholarXiang Yu WangView作者出版物您也可以在

PubMed Google ScholarYing HuView author publicationsYou can also search for this author in

PubMed Google ScholarYing HuView作者出版物您也可以在

PubMed Google ScholarNa ZhangView author publicationsYou can also search for this author in

PubMed Google ScholarNa ZhangView作者出版物您也可以在

PubMed Google ScholarPu-Guang ZhaoView author publicationsYou can also search for this author in

PubMed Google ScholarPu Guang ZhaoView作者出版物您也可以在

PubMed Google ScholarXiao-Mei WeiView author publicationsYou can also search for this author in

PubMed Google ScholarXiao Mei WeiView作者出版物您也可以在

PubMed Google ScholarKun-Hua WeiView author publicationsYou can also search for this author in

PubMed Google ScholarXinya HemuView author publicationsYou can also search for this author in

PubMed Google ScholarXinya HemuView作者出版物您也可以在

PubMed Google ScholarNing-Hua TanView author publicationsYou can also search for this author in

PubMed Google ScholarNing Hua TanView作者出版物您也可以在

PubMed Google ScholarQing-Feng WangView author publicationsYou can also search for this author in

PubMed谷歌学者Qing Feng WangView作者出版物您也可以在

PubMed Google ScholarLing-Yun ChenView author publicationsYou can also search for this author in

PubMed Google ScholarLing Yun ChenView作者出版物您也可以在

PubMed Google ScholarContributionsQ.-F.W., L.-Y.C., K.-H.W., and N.-H.T. designed the research. Q.-F.W., K.-H.W., Y.H., X.-M.W., G.-W.H., X.-X.W., and L.-Y.C. contributed to the taxon sampling and sequencing. X.-X.W., C.-H.H., D.F.M.-B., N.Z., P.-G.Z., X.-Y.H., and L.-Y.C. performed data analyses.

PubMed谷歌学术贡献-F、 W.，L.-Y.C.，K.-H.W。和N.-H.T.设计了这项研究。Q、 -F.W.，K.-H.W.，Y.H.，X.-M.W.，G.-W.H.，X.-X.W。和L.-Y.C.对分类群的采样和测序做出了贡献。十、 -X.W.，C.-H.H.，D.F.M.-B.，N.Z.，P.-G.Z.，X.-Y.H.和L.-Y.C.进行了数据分析。

X.-X.W. performed wet lab experiments. X.-X.W., X.-Y.W., D.F.M.-B., and L.-Y.C. prepared the figures and tables. L.-Y.C. drafted the manuscript. Q.-F.W., C.-H.H., D.F.M.-B., X.-X.W., and L.-Y.C. revised this manuscript. All the authors read this manuscript.Corresponding authorsCorrespondence to.

十、 -X.W.进行了湿实验室实验。十、 -X.W.，X.Y.W.，D.F.M.B。和L.Y.C.准备了数字和表格。五十、 -Y.C.起草了手稿。Q、 -F.W.，C.-H.H.，D.F.M.-B.，X.-X.W。和L.-Y.C.修订了这份手稿。所有作者都阅读了这份手稿。通讯作者通讯。

Kun-Hua Wei, Ning-Hua Tan, Qing-Feng Wang or Ling-Yun Chen.Ethics declarations

魏坤华、谭宁华、王庆峰或陈凌云。道德宣言

Competing interests

相互竞争的利益

The authors declare no competing interests.

作者声明没有利益冲突。

Peer review

同行评审

Peer review information

同行评审信息

Nature Communications thanks Deng-Feng Xie and Mingfang Zhang for their contribution to the peer review of this work. A peer review file is available.

《自然通讯》感谢谢登峰和张明芳为这项工作的同行评审做出的贡献。同行评审文件可用。

Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Supplementary informationSupplementary InformationPeer Review fileDescription of Additional Supplementary FilesSupplementary Data 1-13Reporting SummaryRights and permissions.

Additional informationPublisher的注释Springer Nature在已发布地图和机构隶属关系中的管辖权主张方面保持中立。补充信息补充信息同行评审文件其他补充文件的描述补充数据1-13报告摘要权利和权限。

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material.

开放获取本文是根据知识共享署名非商业性NoDerivatives 4.0国际许可证授权的，该许可证允许以任何媒介或格式进行任何非商业性使用，共享，分发和复制，只要您对原始作者和来源给予适当的信任，提供知识共享许可证的链接，并指出您是否修改了许可材料。

You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

根据本许可证，您无权共享源自本文或其部分的改编材料。本文中的图像或其他第三方材料包含在文章的知识共享许可证中，除非该材料的信用额度中另有说明。如果材料未包含在文章的知识共享许可证中，并且您的预期用途未被法律法规允许或超出允许的用途，则您需要直接获得版权所有者的许可。

To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/..

要查看此许可证的副本，请访问http://creativecommons.org/licenses/by-nc-nd/4.0/..

Reprints and permissionsAbout this articleCite this articleWang, XX., Huang, CH., Morales-Briones, D.F. et al. Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis.

转载和许可本文引用本文Wang，XX。，Huang，CH.，Morales-Briones，D.F.等人。系统转录组学揭示了天冬酰胺的系统发育和葱味生物合成的进化。

Nat Commun 15, 9663 (2024). https://doi.org/10.1038/s41467-024-53943-6Download citationReceived: 23 April 2024Accepted: 29 October 2024Published: 08 November 2024DOI: https://doi.org/10.1038/s41467-024-53943-6Share 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》159663（2024）。https://doi.org/10.1038/s41467-024-53943-6Download引文接收日期：2024年4月23日接受日期：2024年10月29日发布日期：2024年11月8日OI：https://doi.org/10.1038/s41467-024-53943-6Share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。

Provided by the Springer Nature SharedIt content-sharing initiative

由Springer Nature SharedIt内容共享计划提供