J Syst Evol ›› 2021, Vol. 59 ›› Issue (3): 442-453.DOI: 10.1111/jse.12666

• Research Articles • Previous Articles     Next Articles

Resolving robust phylogenetic relationships of core Brassicaceae using genome skimming data

Liang‐Min Liu1,2, Xin‐Yu Du1,2, Cen Guo1, and De‐Zhu Li1,2*   

  1. 1 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
    2 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, Yunnan, China
  • Received:2020-03-20 Accepted:2020-07-24 Online:2020-07-29 Published:2021-05-01

Abstract: The Brassicaceae is an economically and scientifically important family distributed globally, including oilseed rape and the model plant, Arabidopsis thaliana. Although growing molecular data have been used in phylogenetic studies, the relationships among major clades and tribes of Brassicaceae are still controversial. Here, we investigated the core Brassicaceae phylogenetics using 222 plastomes and 235 nrDNA cistrons, including 106 plastomes and 112 nrDNA cistrons assembled from newly sequenced genome skimming data of 112 taxa. The sampling covered 73 genera from 61.5% tribes and four unassigned genera and species. Three well supported lineages LI, LII, and LIII were revealed in our plastomic analyses, with LI sister to LII + LIII. In addition, the monophyly of the newly delimitated LII was strongly supported by three different partition strategies, concatenated methods under Bayesian and Maximum Likelihood analyses. LII comprised 13 tribes, including four tribes previously unassigned to any lineage, that is Biscutelleae as the earliest diverging clade and Cochlearieae as the sister to Megacarpaeeae + Anastaticeae. Within LII, the intertribal relationships were also well resolved, except that a conflicting position of Orychophragmus was detected among different datasets. In LIII, Shehbazia was resolved as a member of Chorisproreae, but Chorisproreae, Dontostemoneae, and Euclidieae were all resolved as paraphyletic, which was also confirmed by nrDNA analyses. Moreover, the loss of the rps16 gene was detected as likely to be a synapomorphy of the tribes Arabideae and Alysseae. Overall, using genome skimming data, we resolved robust phylogenetic relationships of core Brassicaceae and shed new light on the complex evolutionary history of this family.

Phylogenetic relationship of the core Brassicaceae based on the plastome-scale dataset, showing three well-supported lineages LI, LII, and LIII, with LI sister to LII +  LIII. The newly delimitated LII was strongly supported as monophyletic, with Biscutelleae as the earliest diverging clade, and in LIII, Shehbazia was resolved as a member of Chorisproreae. The present/absent genes (in blue/pink boxes) of this diagram indicated that the loss of the rps16 gene was likely a synapomorphy of the tribes Arabideae and Alysseae.
Photographs by Liang-Min Liu, Xin-Yu Du, Cen Guo, and De-Zhu Li. Designed by Liang-Min Liu, Xin-Yu Du, Cen Guo, and De-Zhu Li.

Key words: core Brassicaceae, incongruence, nuclear ribosome DNA, plastid genome