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Summary Although horizontal gene transfer (HGT) is common in angiosperm mitochondrial DNAs (mtDNAs), few cases of functional foreign genes have been identified. The one outstanding candidate for large‐scale functional HGT is the holoparasite Lophophytum mirabile, whose mtDNA has lost most native genes but contains intact foreign homologs acquired from legume host plants. To investigate the extent to which this situation results from functional replacement of native by foreign genes, functional mitochondrial gene transfer to the nucleus, and/or loss of mitochondrial biochemical function in the context of extreme parasitism, we examined the Lophophytum mitochondrial and nuclear transcriptomes by deep paired‐end RNA sequencing. Most foreign mitochondrial genes in Lophophytum are highly transcribed, accurately spliced, and efficiently RNA edited. By contrast, we found no evidence for functional gene transfer to the nucleus or loss of mitochondrial functions in Lophophytum. Many functional replacements occurred via the physical replacement of native genes by foreign genes. Some of these events probably occurred as the final act of HGT itself. Lophophytum mtDNA has experienced an unprecedented level of functional replacement of native genes by foreign copies. This raises important questions concerning population‐genetic and molecular regimes that underlie such a high level of foreign gene takeover.

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Helosis cayennensis (Balanophoraceae s.str.) is a holoparasite characterised by aberrant vegetative bodies and tiny, reduced unisexual flowers. Here, we analysed the development of female flowers to elucidate their morpho-anatomy and the historical controversy on embryo sac formation. We also studied the developmental origin of inflorescences and the ontogeny of fruits, embryo and endosperm and discussed in a phylogenetic framework. Inflorescences were analysed by optical, fluorescence and scanning electron microscopy. Inflorescences of H. cayennensis arise endogenously. Female flowers lack perianth organs, thus only consist of the ovary, two styles and stigmata. Ovules are undifferentiated; two megaspore mother cells develop inside a nucellar complex. The female gametophyte, named Helosis-type, is a bisporic four-celled embryo sac, provided with a typical egg apparatus and a uni-nucleated central cell. Fertilization was not observed, yet a few-celled embryo and cellular endosperm developed. In sum, results confirm that, among Santalales holoparasites, Helosis is intermediate in the reduction series of its floral organs. Although perianth absence best supports the Balanophoraceae s.str. clade, our literature survey on female flower developmental data across Balanophoraceae s.l. highlights the many gaps that need to be filled to really understand these features in the light of new phylogenetic relationships.

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