Premise To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target‐enriched nuclear data to improve our understanding of phylogenetic relationships in the family. Methods We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in Brunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to infer Brunellia phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral‐state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in Brunellia. Results Brunellia comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses. Conclusions Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene‐tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character‐state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in Brunellia, the relationships among subclades remain incompletely understood.

Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.

The transfer of DNA among distantly related organisms is relatively common in bacteria but less prevalent in eukaryotes. Among fungi and plants, few of these events have been reported. Two segments of fungal mitochondrial DNA have been recently discovered in the mitogenome of orchids. Here, we build on that work to understand the timing of those transfer events, which orchids retain the fungal DNA and the fate of the foreign DNA during orchid evolution. We update the content of the large DNA fragment and establish that it was transferred to the most recent common ancestor of a highly diverse clade of epidendroid orchids that lived ~28–43 Mya. Also, we present hypotheses of the origin of the small transferred fragment. Our findings deepen the knowledge of these interesting DNA transfers among organelles and we formulate a probable mechanism for these horizontal gene transfer events.

The chloroplast (plastid) controls carbon uptake, so its DNA sequence and function are highly conserved throughout the land plants. But for those that have alternative carbon supplies, the plastid genome is susceptible to suffer mutations in the photosynthetic genes and overall size reduction. Fully mycoheterotrophic plants receive organic carbon from their fungi partner, do not photosynthesize and also do not exhibit green coloration (or produce substantial quantities of chlorophyll). Epipactis helleborine (L.) Crantz exhibits all trophic modes from autotrophy to full mycoheterotrophy. Albinism is a stable condition in individuals of this species and does not prevent them from producing flowers and fruits. Here we assemble and compare the plastid genome of green and albino individuals. Our results show that there is still strong selective pressure in the plastid genome. Therefore, the few punctual differences among them, to our knowledge, do not affect any normal photosynthetic capability in the albino plant. These findings suggest that mutations or other genetically controlled processes in other genomes, or environmental conditions, are responsible for the phenotype.