Plastome evolution in Santalales involves relaxed selection prior to loss of ndh genes and major boundary shifts of the inverted repeat.

Background and aims: Biological aspects of haustorial parasitism have significant effects on the configuration of the plastid genome. Approximately half the diversity of haustorial parasites belongs to the order Santalales, where a clearer picture of plastome evolution in relation to parasitism is starting to emerge. However, in previous studies of plastome evolution there is still a notable under-representation of members from non-parasitic and deep-branching hemiparasitic lineages, limiting evolutionary inference around the time of transition to a parasitic lifestyle. To expand taxon sampling relevant to this transition we therefore targeted three families of non-parasites (Erythropalaceae, Strombosiaceae, and Coulaceae), two families of root-feeding hemiparasites (Ximeniaceae and Olacaceae), and two families of uncertain parasitic status (Aptandraceae and Octoknemaceae). With data from these lineages we aimed to explore plastome evolution in relation to evolution of parasitism.

Methods: From 29 new samples we sequenced and annotated plastomes and the nuclear ribosomal cistron. We examined phylogenetic patterns, plastome evolution, and patterns of relaxed or intensified selection in plastid genes. Available transcriptome data were analyzed to investigate potential transfer of infA to the nuclear genome.

Results: Phylogenetic relationships indicate a single functional loss of all plastid ndh genes (ndhA-K) in a clade formed by confirmed parasites and Aptandraceae, and the loss coincides with major size and boundary shifts of the inverted repeat (IR) region. Depending on an autotrophic or heterotrophic lifestyle in Aptandraceae, plastome changes are either correlated with or predate evolution of parasitism. Phylogenetic patterns also indicate repeated loss of infA from the plastome, and based on presence of transcribed sequences with presequences corresponding to thylakoid luminal transit peptides, we infer that the genes were transferred to the nuclear genome.

Conclusions: Except for the loss of the ndh complex, relatively few genes have been lost from the plastome in deep-branching root parasites in Santalales. Prior to loss of the ndh genes, they show signs of relaxed selection indicative of their dispensability. To firmly establish a potential correlation between ndh gene loss, plastome instability and evolution of parasitism, it is pertinent to refute or confirm a parasitic lifestyle all Santalales clades.