While the evolution of mitochondrial protein-coding genes in angiosperms has been extensively studied, the post-transcriptional RNA processing remains under-explored. Leveraging newly generated and public RNA-seq data from twenty representative angiosperms, we systematically inferred the gain-and-loss dynamics of RNA editing sites within mitochondrial protein-coding genes. Our findings reveal magnoliids retain more ancestral RNA editing sites compared to monocots and eudicots. Furthermore, we uncovered contrasting correlations between gene expression levels and RNA editing density: negative in core mitochondrial genes but positive in variable genes. We also identified widespread occurrence of stop codon-lacking transcripts of four genes (ccmC, nad6, sdh3 and sdh4) across angiosperms, a phenomenon mainly reported in Arabidopsis thaliana. Besides the known t-element previously identified in A. thaliana, we revealed another distinct motif that may contribute to the post-transcriptional processing of nad6 transcripts. Novel stem-loop motifs that may mediate the formation of stop codon-lacking transcripts of ccmC, sdh3 and sdh4 genes were also identified. Collectively, our study sheds light on the ancestral RNA editing characteristics of angiosperm mitochondrial genes, and provides evidence that the processing-derived stop codon-lacking transcripts predate the divergence of angiosperms.

Summary: Horizontal gene transfer (HGT), a well-established driver of genome evolution in prokaryotes, was historically considered rare in plants. However, accumulating genomic evidence supports its occurrence in angiosperms, impacting both nuclear and mitochondrial genomes, particularly in parasitic species that establish vascular connections with their hosts. Despite the increasing recognition of HGT in a few clades of parasitic plants (e.g., Balanophoraceae, Rafflesiaceae, and Cynomoriaceae), the underlying mechanisms and evolutionary consequences of these transfers are still not fully understood. Mitrastemon yamamotoi , a holoparasitic endoparasite in the order Ericales, invades the roots of host trees in the Fagaceae family, creating favorable conditions for HGT. In this study, we assembled for the first time the mtDNA of Mitrastemon , revealing a multipartite structure consisting of 51 circular-mapping chromosomes. Phylogenetic and comparative genomic analyses uncovered extensive HGT from Fagaceae hosts, affecting both coding and non-coding regions. Notably, more than 60% of the Mitrastemon mtDNA is of foreign origin, and seven chromosomes are entirely foreign, with structural signatures in the donor mtDNA consistent with the recently proposed circle-mediated HGT model. Additionally, we detected six protein-coding genes of foreign origin and one chimeric gene. Remarkably, a foreign atp1 gene has replaced the missing native copy and represents a rare event of functional HGT in plant mitochondria. These results position Mitrastemon as a valuable model for studying mtDNA evolution and deepening our understanding of the HGT process. Our findings expand the range of lineages in which circle-mediated HGT has been documented, suggesting it is a more widespread and fundamental mode of mitochondrial HGT in plants. Significant Statement: Parasitic plants form intimate connections with their hosts, but how these interactions influence genome evolution remains poorly understood. Our study shows that Mitrastemon yamamotoi has acquired over 60% of its mitochondrial DNA from its host through horizontal gene transfer, including entire foreign chromosomes. These findings provide strong support for a recently proposed mechanism, circle-mediated HGT, and suggest that this process may be a more widespread driver of mitochondrial genome evolution in flowering plants.

Background and Aims: In heterotrophic plants, the loss of photosynthesis is often associated with plastid genome (ptDNA) reduction, although the extent of genome decay varies widely among lineages and may culminate in complete genome loss. Of the multiple transitions to heterotrophy among angiosperms, the ptDNA status remains poorly defined in lineages such as the endoparasitic Mitrastemonaceae (Ericales). Methods: Adopting a panplastome perspective, we characterized genomic variation across Mitrastemon yamamotoi individuals, assembling two complete circular ptDNAs and re-evaluating all available genomic resources for the species. Results: Our results reveal a highly minimized ptDNA (18–26 kb) with elevated AT content (>77 %) and loss of the typical quadripartite architecture. The M. yamamotoi panplastome exhibits remarkable structural stability and collinearity among individuals. The reduced plastid gene set comprises 26 genes, including accD, infA, clpP, ycf1, ycf2 and the essential tetrapyrrole precursor trnE−UUC. Root-to-tip substitution-rate analyses of 13 conserved protein-coding genes revealed elevated synonymous and non-synonymous substitution rates in M. yamamotoi relative to photosynthetic angiosperms. However, dN/dS analyses showed that the retained protein-coding genes evolve under purifying selection (ω < 1), indicating persistent functional constraint. Furthermore, transcriptomic analysis identified a nearly complete set of nuclear-encoded plastid-targeted DNA-RRR factors, with the notable exception of the MUTS2 surveillance system and two photolyases. The convergent loss of MUTS2 homologues in M. yamamotoi and holoparasitic Balanophoraceae may be linked to shared plastome features (genome compaction, accelerated substitution rates, and severe AT bias). In contrast, the shared loss of the photolyases CRY3 and UVR3 likely results from relaxed selection pressure associated with an underground lifestyle. Conclusions: Deciphering the M. yamamotoi panplastome provides a definitive genomic framework for understanding plastid evolution within the endoparasitic Mitrastemonaceae.