J Integr Plant Biol. ›› 2023, Vol. 65 ›› Issue (2): 299-323.DOI: 10.1111/jipb.13415

• Invited Expert Reviews • Previous Articles     Next Articles

Phylogenomics and the flowering plant tree of life

Cen Guo1, Yang Luo2, Lian-Ming Gao2,3, Ting-Shuang Yi1,2, Hong-Tao Li1, Jun-Bo Yang1 and De-Zhu Li1,2,3,4*   

  1. 1. Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China;
    2. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China;
    3. Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China;
    4. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, China
    *Correspondence: De‐Zhu Li (dzl@mail.kib.ac.cn)
  • Received:2022-09-09 Accepted:2022-11-22 Online:2022-11-23 Published:2023-02-01

Abstract: The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.

Key words: angiosperms, hybridization, incomplete lineage sorting, orthology inference, phylogenetic conflicts, reduced representation sequencing, whole-genome sequencing, whole-genome duplication

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