Resolving robust phylogenetic relationships of core Brassicaceae using genome skimming data

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.

Hemilophia cardiocarpa (Brassicaceae), a new species from Yunnan, southwest China

“…The systematic position of Hemilophia in Brassicaceae is not well resolved up to now. Schulz (1936) placed it in the tribe Lepidieae DC., whereas this treatment was not supported by recent studies ( Al-Shehbaz 2012 ; Nikolov et al 2019 ; Walden et al 2020 ; Francis et al 2021 ; Liu et al 2021 ).…”

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

“…However, the deeper nodes within the Brassicaceae family –reflecting the position of the five main lineages of the core Brassicaceae– have been notoriously hard to recover in the past. Some authors have claimed to have solved the true Brassicaceae backbone derived from an NGS dataset (Liu et al 2020), but relied only on bootstrap and posterior probability values. However, we show that alternative sampling routines can recover high bootstrap and posterior probability values on conflicting topologies (supplementary table S5), questioning the value of these support metrics.…”

Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species

“…The chloroplast genome sequences of 40 Theaceae species were aligned using the Muitiple Sequence Alignment Program (MAFFT v.7.4.0) ( Katoh and Standley, 2013 ). The Maximum Likelihood phylogenetic tree of 40 Theaceae species was constructed with RAxML v.8.2.12 ( Stamatakis, 2014 ) with 1000 bootstrap replicates, referring to the method of Liu et al (2021) . Other parameters were set by default in the software.…”