Comparative Analyses of Chloroplast Genomes for Parasitic Species of Santalales in the Light of Two Newly Sequenced Species, and .

When a flowering plant species changes its life history from self-supply to parasite, its chloroplast genomes may have experienced functional physical reduction, and gene loss. Most species of Santalales are hemiparasitic and few studies focus on comparing the chloroplast genomes of the species from this order. In this study, we collected and compared chloroplast genomes of 12 species of Santalales and sequenced the chloroplast genomes of and for the first time. The chloroplast genomes for these species showed typical quadripartite structural organization. Phylogenetic analysis suggested that these 12 species of Santalales clustered into three clades: (4 spp.) and (1 sp.) in the Santalaceae and (1 sp.) in the Opiliaceae formed one clade, while (3 spp.) and (1 sp.) in the Loranthaceae and (1 sp.) in the Schoepfiaceae formed another clade. (1 sp.), in the Erythropalaceae, appeared as a third, most distant, clade within the Santalales. In addition, both and are monophyletic, and is sister to . A comparative analysis of the chloroplast genome showed differences in genome size and the loss of genes, such as the genes, genes, partial ribosomal genes, and tRNA genes. The 12 species were classified into six categories by the loss, order, and structure of genes in the chloroplast genome. Each of the five genera (, , , , and ) represented an independent category, while the three species and were classified into a sixth category. Although we found that different genes were lost in various categories, most genes related to photosynthesis were retained in the 12 species. Hence, the genetic information accorded with observations that they are hemiparasitic species. Our comparative genomic analyses can provide a new case for the chloroplast genome evolution of parasitic species.