Phylogenomics clarifies Balanophora evolution, metabolic retention in reduced plastids, and the origins of obligate agamospermy

Summary Holoparasitic plants are nongreen plants that depend entirely on their host plants for essential resources. The transition to parasitism often results in functional reduction and gene loss, but its timing and extent remain unclear. Although Balanophora is known to have extremely reduced plastid genomes, only five species from a few geographically restricted regions have been studied. Here, we sampled seven species from 12 populations across Taiwan and Japan, assembled their plastomes and transcriptomes, and inferred multigene trees from diverse plastid and nuclear markers. To understand the plastid's functional role, we predicted the subcellular localization of nuclear‐encoded proteins. All the plastid genomes are reduced to 14–16 kb. They are colinear, AT‐biased (87–88%), and share the same noncanonical genetic code (TAG→Trp). Phylogenomics of Balanophora implies independent origins of obligate agamospermy in island populations of several species. Over 700 Balanophora proteins were predicted to be plastid‐targeted, suggesting retained capacity for the biosynthesis of amino acids, fatty acids, riboflavin, and other pathways. The plastid genome reduction occurred before the diversification of Balanophora . Similar to other parasites, it primarily erased photosynthesis‐related functions without massive elimination of other functions. Balanophoraceae thus emerge as a fascinating model for reconstructing the evolutionary changes associated with photosynthesis loss in land plants.