Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Premise : Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels, but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome.

Methods : We present a phylogenomic examination of a major angiosperm clade ( Asteridae ) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group.

Results : We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinops...