A comprehensive phylogenomic platform for exploring the angiosperm Tree of Life
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Abstract The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96$\%$) and 2333 genera (17$\%$). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]
摘要 生命之树是探索地球生命演化历程与生物学属性的核心路线图，但目前仍有大量未知领域亟待发掘。即便对于被子植物（angiosperms，flowering plants）而言，尽管其在维系陆地生态系统稳定中扮演着关键角色，相关研究仍存在诸多数据缺口。当下，高通量测序技术有望大幅深化我们对生物演化亲缘关系的认知。本文介绍一套用于探究被子植物生命之树的综合系统基因组学平台，该平台基于通用被子植物353（Angiosperms353）序列捕获探针靶向的353个核基因，搭建了一套开放工具与数据体系。本文的核心目标有三：其一，完整记录本研究采用的方法；其二，介绍首批公开数据的发布情况；其三，呈现一款全新的开放数据门户——邱园生命之树探索器（Kew Tree of Life Explorer，https://treeoflife.kew.org）。本团队计划针对所有被子植物属级类群生成全新的靶向序列捕获数据，将充分利用标本馆标本等自然历史馆藏资源，并结合从公开数据库中挖掘得到的现有数据。本次公布的首批数据是目前为止规模最大的被子植物核系统基因组学数据集，包含经DNA条形码与系统发育检验验证的3099份样本，涵盖全部64个目、404个科（占比96%）以及2333个属（占比17%）。研究团队基于总计824878条序列、489086049个碱基对与532260个比对位点，推断出首版被子植物生命之树，并将其交互式呈现于邱园生命之树探索器中。该物种树的构建方法严谨且适配当前的项目规模。尽管在类群与基因采样、基因回收率、序列演化模型以及旁系同源基因处理方面仍存在局限，但该生命之树有力支持了现有分类学体系，同时对诸多已提出的目级亲缘关系假说提出挑战，并首次明确了众多属类的系统发育位置。经验证的数据集、物种树及所有中间产物均可通过邱园生命之树探索器公开获取，并将在后续新增数据时持续更新。这一朝着完成所有被子植物物种完整生命之树迈进的重要里程碑，将通过标准化核标记的系统性测序，为被子植物系统基因组学开启高度整合的未来发展路径。本研究方案有望成为两大领域间亟需的桥梁：一方面是全球范围内测序所有地球生物基因组的研究浪潮，另一方面则是全球自然历史馆藏所蕴含的巨大系统基因组学潜力。[关键词：被子植物；Angiosperms353；基因组学；标本馆组学；馆藏组学；核系统基因组学；开放获取；靶向序列捕获；生命之树]
