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Background  Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes.    Results  In order to facilitate further studies of cytonuclear interactions in  Eucalyptus , we report an updated annotation of the  E. grandis  plastid genome, and the second sequenced and annotated mitochondrial genome of the Myrtales, that of  E. grandis . The 478,813 bp mitochondrial genome shows the conserved protein coding regions and gene order rearrangements typical of land plants. There have been widespread insertions of organellar DNA into the  E. grandis  nuclear genome, which span 141 annotated nuclear genes. Further, we identify predicted editing sites to allow for the discrimination of RNA-sequencing reads between nuclear and organellar gene copies, finding that nuclear copies of organellar genes are not expressed in  E. grandis .    Conclusions  The implications of organellar DNA transfer to the nucleus are often ignored, despite the insight they can give into the ongoing evolution of plant genomes, and the problems they can cause in many applications of genomics. Future comparisons of the transcription and regulation of organellar genes between  Eucalyptus  genotypes may provide insight to the cytonuclear interactions that impact economically important traits in this widely grown lignocellulosic crop species.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5444-4) contains supplementary material, which is available to authorized users.

The plastid and mitochondrial genomes of Eucalyptus grandis