Abstract
BackgroundLand 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.ResultsIn 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.ConclusionsThe 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.
Highlights
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
Genome structure and gene content of the E. grandis mitochondrial genome We used mitochondrial genome scaffolds from the Joint Genome Institute assembly of the E. grandis nuclear genome to perform a reference-based assembly of the mitochondrial genome from Illumina whole genome sequencing (WGS) data
The average coverage of the WGS reads across the mitochondrial genome is ~ 700, with regions of ten times the average coverage representing overlaps between the plastid and mitochondrial genomes (Fig. 1b) Repeat elements make up 2.47% of the E. grandis mitochondrial genome, consisting mainly of simple and low complexity repeats (Table 1, Additional file 1: Table S1)
Summary
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. Intracellular DNA transfer results in nuclear plastidial DNAs (NUPTs) and nuclear mitochondrial DNAs (NUMTs), that are still present in the organellar genomes [4]. The rate and distribution of organellar inserts into the nuclear genome vary between plant species, as do the location and proximity to transposable elements, which rearrange and expand inserted regions [10]. These recent inter-genomic DNA transfers between the nuclear
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
