Plastid phylogenomics of the parietal clade of Malpighiales: ancestral genome synteny and congruent signal across exons, introns and spacers in support of Salicaceae relationships.

Background and aims: The parietal clade is one of the major lineages of the angiosperm order Malpighiales. Several nodes in the phylogenetic trees inferred from concatenated chloroplast genes exhibited low support, and various Malpighiales genera were found to have highly altered plastid genomes.

Methods: Here we newly generated seven complete plastid genomes to represent the major lineages of the pantropical genus Casearia using genome skimming. Together with published genome sequences of various sources, we comparatively analysed the genome structure of all major lineages of the Salicaceae and their putative relatives across the parietal clade.

Key results: All plastid genomes, including those of the Rhizophoraceae outgroup, were syntenous, with the exception of Passifloraceae, which exhibited accelerated pseudogenization, gene loss and major structural rearrangements. Although rpl32 is absent from all Salicaceae, this is not a synapomorphy for the family, due to other losses in genera such as Hydnocarpus and Viola. Apart from the exons, we found sequences of all introns and most spacers to be alignable, except short and hypervariable stem-loop elements. We could therefore explore the phylogenetic signal of complete plastid genomes.

Conclusions: All three partitions, exons, introns and spacers, presented congruent topologies with maximum support for the Samydoideae being sister to a clade of Salicoideae and Scyphostegioideae within the monophyletic Salicaceae. Our results underscore the potential of complete plastid genomes to further explore the evolutionary diversification of the Malpighiales.