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利用转录组和基因组数据集的核基因解决深被子植物系统发育及其时间多样化问题。

花匠小妙招
2026-01-31 05:03

利用转录组和基因组数据集的核基因解决深被子植物系统发育及其时间多样化问题。

Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.

机构信息

State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.

Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA.

出版信息

New Phytol. 2017 May;214(3):1338-1354. doi: 10.1111/nph.14503. Epub 2017 Mar 14.

Abstract

Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots.

摘要

真核生物的爆发式多样化现象非常普遍，这使得解析系统发育关系变得非常困难。被子植物包含了现存开花植物的约 75%，对人类生活和陆地生态系统非常重要，并且可能经历了爆发式多样化。被子植物的系统发育关系，特别是五桠果亚纲的系统发育关系，仍然没有得到解决。在这里，我们使用 31 个新生成的转录组和 88 个其他数据集（涵盖了 70%的被子植物目），提出了一个高度支持的被子植物系统发育和多样化率变化的结果。一个高度支持的被子植物系统发育将五桠果亚纲分为两组：一组包括蔷薇目、虎耳草目、卫矛目和檀香目；另一组包含了石竹目、十字花目和铁青树科，而对水马齿目则存在不确定性。分子钟分析估计，被子植物冠群起源于约 1.46 亿年前，比最早的三沟花粉化石和大多数其他分子钟估计都要早得多，而五桠果亚纲在约 1500 万年内依次分化为八个主要谱系。两个已确定的多样化率增加的位置位于五桠果亚纲和石竹目所在的茎干中，并且滞后于γ六倍体化。从新生成的转录组中提取的核基因揭示了一个高度解析的被子植物系统发育关系，主要核心被子植物谱系的顺序分离以及多样化的时间模式，为理解形态进化趋势和被子植物多样化的贡献提供了新的见解。

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