Comparative plastomes of five species: genome organization, structural features, and patterns of pseudogenization and gene loss.

The evolution of heterotrophic lifestyle entails varying degrees of plastome degradation. Yet, the evolutionary trajectory of plastome degradation associated with parasitism remains poorly explored in hemiparasites. We sequenced, assembled, and annotated the complete plastomes of five species of mistletoes. In addition, publicly available plastomes of 58 species in Loranthaceae were obtained and re-annotated for phylogenetic and comparative analyses. We used a comparative phylogenetic approach to evaluate whether patterns of pseudogenization and gene loss differ among lineages of hemiparasites in Loranthaceae. Gene order was highly conserved, with higher sequence similarity and structural conservation between closely related species but with considerable plastome size variation (from 121 238 to 125 427 bp). The expansion and contraction at the borders of inverted repeats (IRs) and intergenic regions variation greatly contribute to size variations among plastomes. Phylogenetic analysis of plastomes of 60 species in Loranthaceae including 5 species of the previously unsampled tribe Psittacantheae was largely congruent with previous phylogenetic studies. The loss of most of the complex (10 out of 11 genes), , , and genes, was identified in all studied species. Also, the loss and pseudogenization of and genes in were uncommon in other Loranthaceae species. The structural variation uncovered in plastomes reveals that, despite high synteny, significant size variation exists among species. This variation can be attributed to processes such as variations in the length of intergenic regions and the expansion/contraction of IR borders, traits that have been comparatively understudied in earlier Loranthaceae works.