J Integr Plant Biol. ›› 2023, Vol. 65 ›› Issue (6): 1479-1489.DOI: 10.1111/jipb.13455

• Molecular Ecology and Evolution • Previous Articles     Next Articles

Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets

Hongyin Hu1†, Pengchuan Sun2†, Yongzhi Yang1†, Jianxiang Ma1 and Jianquan Liu1,2*   

  1. 1. State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
    2. Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
    Hongyin Hu, Pengchuan Sun and Yongzhi Yang contributed equally to this work.
    *Correspondence:Jianquan Liu(liujq@nwipb.cas.cn)
  • Received:2022-10-10 Accepted:2023-01-16 Online:2023-01-16 Published:2023-06-01

Abstract: Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

Key words: angiosperms, divergence times, genomic, phylogenomics

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