A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.
复制标题
探索被子植物生命树的综合系统基因组平台。
DOI：
10.1093/sysbio/syab035
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发表时间：
2022-02-10
影响因子：
6.5
通讯作者：
Forest F
中科院分区：
文献类型：
--
作者：
Baker WJ;Bailey P;Barber V;Barker A;Bellot S;Bishop D;Botigué LR;Brewer G;Carruthers T;Clarkson JJ;Cook J;Cowan RS;Dodsworth S;Epitawalage N;Françoso E;Gallego B;Johnson MG;Kim JT;Leempoel K;Maurin O;Mcginnie C;Pokorny L;Roy S;Stone M;Toledo E;Wickett NJ;Zuntini AR;Eiserhardt WL;Kersey PJ;Leitch IJ;Forest F
生命之树是导航地球上生命进化和特性的基本生物学路线图，但在很大程度上仍不为人所知。即使是被子植物（开花植物），尽管它们在维持陆地生命中起着至关重要的作用，但也充满了数据空白。如今，高通量测序有望显著加深我们对进化关系的理解。在这里，我们描述了一个全面的系统基因组平台，用于探索被子植物的生命之树，包括一套基于通用被子植物353序列捕获探针靶向的353个核基因的开放工具和数据。本文的主要目标是(i)记录我们的方法，（ii）描述我们的第一个数据发布，以及（iii）介绍一个新颖的开放数据门户，邱园生命之树探索者（https://treeoflife.kew.org）。我们的目标是为所有属的开花植物生成新的目标序列捕获数据，利用自然历史收藏品，如植物标本馆标本，并与挖掘的公共数据进行增强。我们的第一个数据发布，在这里描述，是迄今为止最广泛的被子植物核系统发育数据集，包括3099个样本，通过DNA条形码和系统发育测试验证，代表所有64目，404科（96）和2333属（17）。从总共824,878个序列、489,086,049个碱基对和532,260个比对列的数据中推断出“第一遍”被子植物生命树，并在邱园生命树探索者中进行交互式展示。这个物种树是用严格的方法生成的，但在我们的操作规模下是容易处理的。尽管在分类群和基因采样、基因恢复、序列进化模型和相似性方面存在局限性，但该树强烈支持现有的分类学，同时挑战了许多目之间的假设关系，并首次放置了许多属。经过验证的数据集、物种树和所有中间体都可以通过邱园生命之树探索者公开访问，并将在获得更多数据时进行更新。这一重要的里程碑为所有开花植物物种的完整生命之树打开了大门，通过标准化核标记的系统测序，被子植物系统基因组学将高度整合。我们的方法有潜力在日益增长的地球上所有生命基因组测序运动和世界自然历史收藏的巨大系统基因组学潜力之间架起一座急需的桥梁。(被子植物;Angiosperms353;基因组学;herbariomics;museomics;核phylogenomics;开放存取;目标序列捕获；生命之树。
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.]
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