Plant Systematics and Evolution

, Volume 303, Issue 3, pp 413–417 | Cite as

Phylogenetic analysis of 25 plant species representing 19 angiosperm families and one gymnosperm family based on 390 orthologous genes

  • Mengjun LiuEmail author
  • Jin Zhao
  • Jiurui Wang
  • Zhiguo Liu
  • Guocheng Liu
Original Article


High-throughput sequencing is fundamentally altering traditional phylogenetic classifications. While the Angiosperm Phylogeny Group (APG) III system based on chloroplast sequences has opened up a new era of angiosperm molecular classification, the use of nuclear genome sequences is more helpful for a precise phylogenetic analysis. However, such attempts have so far been applied to only a very limited number of angiosperm plant families. We constructed a phylogenetic tree of 25 plant species with well assembled genome sequences representing 19 angiosperm families and one gymnosperm family (as out group) using 390 orthologous genes. Our results strongly support the moving of Rhamnaceae to order Rosales from Rhamnales, abolishing Rhamnales, and establishing the new order Malpighiales in the APG III system. Our data also showed some characteristics inconsistent with the APG III classification and provided a reinterpretation of phylogeny for some of the families involved. We propose that Malpighiales should be placed in Malvids, not Fabids. The four monocot species representing four families were clustered together, indicating that monocot is a natural taxon. In summary, our results support almost all the APGIII treatments of the orders involved in this study and provided some surprising reinterpretations at levels beyond order.


Angiosperm APG III system Genome sequence Orthologous genes Phylogenetic tree 



This work was supported by grants from the National Science and Technology Support Plan of China (2013BAD14B03), The Giant Plan of Hebei, China, and The Top Talent Project of Hebei, China and Agricultural University of Hebei Foundation for Leaders of Disciplines in Science Technology. We thank Dr. Peter Gorsuch, Dr. Laurie Goodman as well as MSC Scientific Editing and American Journal Experts for their kind assistance with manuscript revisions.

Compliance with ethical standards

Conflict of interest

The author declares that he has no conflict of interest.

Supplementary material

606_2016_1380_MOESM1_ESM.txt (15.2 mb)
Online Resource 1 Sequence information of the 390 orthologous genes from 25 plant species used in this study.
606_2016_1380_MOESM2_ESM.pdf (189 kb)
Online Resource 2 Phylogenetic relationships among 21 plant species (only one single Rosaceae species is used) representing 19 angiosperm families and one gymnosperm family. The phylogenetic tree was constructed using 390 orthologous genes by the maximum likelihood method on 4-fold degenerate sites.


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Copyright information

© Springer-Verlag Wien 2017

Authors and Affiliations

  • Mengjun Liu
    • 1
    • 2
    Email author
  • Jin Zhao
    • 3
  • Jiurui Wang
    • 4
  • Zhiguo Liu
    • 1
  • Guocheng Liu
    • 5
  1. 1.Research Center of Chinese JujubeHebei Agricultural UniversityBaodingChina
  2. 2.Beijing Collaborative Innovation Center for Eco-environmental Improvement With Forestry and Fruit TreesBeijingChina
  3. 3.College of Life ScienceHebei Agricultural UniversityBaodingChina
  4. 4.College of ForestryHebei Agricultural UniversityBaodingChina
  5. 5.BGI-ShenzhenShenzhenChina

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