A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)

Whole genome duplication events are notably widespread in plants and this
poses particular challenges for phylogenetic inference in allopolyploid
lineages, i.e. lineages that result from the merging of two or more
diverged genomes after interspecific hybridization. The nuclear genomes
resulting from allopolyploidization contain homologous gene copies from
different evolutionary origins called homoeologs, whose orthologs must be
sorted out in order to reconstruct the evolutionary history of polyploid
clades. In this study, we propose a methodological approach to resolve the
phylogeny of allopolyploid clades focusing on mesopolyploid genomes, which
experienced some level of genome reshuffling and gene fractionation across
their subgenomes. To illustrate our methodological framework, we applied
it to a clade belonging to the model Brassicaceae plant family, the
Brassiceae tribe, that experienced a mesohexaploidy event. The dataset
analysed consists of both publically available genomic sequences and new
transcriptomic data according to taxa. The present methodology requires a
well-annotated reference genome, for which the identification of the
parental subgenome fragments has been performed (e.g. Brassica rapa and
Brassica oleracea). Focusing on fully retained genes (i.e., genes for
which all homoeologous gene copies inherited from the parental lineages
are still present in the reference genome), the method constructs
multilabelled gene trees that allow subsequent assignment of each gene
copy to its diploid parental lineage. Once the orthologous copies are
identified, genes from the same parental origin are concatenated and
tree-building methods are used to reconstruct the species tree. This
method allows resolving the phylogenetic relationships (i) among extant
species within a mesopolyploid clade, (ii) among the parental lineages of
a mesopolyploid lineage, and (iii) between the parental lineages and
closely related extant species. We report here the first well-resolved
nuclear-based phylogeny of the Brassiceae tribe.