Pinard, DesreMyburg, Alexander AndrewMizrachi, Eshchar2020-07-112020-07-112019-02-13Pinard, D., Myburg, A.A. & Mizrachi, E. 2019, 'The plastid and mitochondrial genomes of Eucalyptus grandis', BMC Genomics, vol. 20, art. 132, pp. 1-14.1471-2164 (online)10.1186/s12864-019-5444-4http://hdl.handle.net/2263/75145Additional file 1: Table S1. E. grandis mitochondrial and plastid genome short repeat elements overviewAdditional file 2: Excel spreadsheet of the results of UniPro UGENE analysis of large (length > 100 bp, identity > 95%) repeats in the Eucalyptus grandis mitochondrial genome.Additional file 3: Excel spreadsheet of the results of SVDetect analysis results showing breakpoints of structural variants in the E. grandis mitochondrial genome (Sheet 1), and breakpoints within 250 bp of mitochondrial genome large repeat regions (Sheet 2).Additional file 4: Figure S1. Discordantly mapped read pairs flanking direct repeat 13 of the mitochondrial genome. The insert size of the reads is ~ 118,000 bp, compared to the expected 475. These reads suggest a repeat mediated structural variation, supported by SVDetect analysis. Read pair insert is shown by the red lines and the direct repeat is shown in the blue track.Additional file 5: Figure S2. Mitochondrial genome gene order comparison between Eucalyptus grandis and Lagerstroemia indica. The gene order for the E. grandis mitochondrial genome is shown at the right of the figure, and that of L. indica on the top. Genes that are not found in each genome are indicated with red text. Collinear genes are indicated by red boxes.Additional file 6: Figure S3. Multiple whole genome alignment of selected land plant mitochondrial genomes. Alignment was performed using the progressiveMauve algorithm in Mauve multiple alignment tool [87], with the coloured blocks representing Locally Collinear Blocks of sequences between genomes. The red lines indicate the length of the mitochondrial genomes, and the name of the organism is shown at the bottom of each genome. This figure shows the widespread genome rearrangements present in plant mitochondrial genomes.Additional file 7: Excel spreadsheet of the results of predicted editing sites in the E. grandis mitochondrial (Sheet 1) and plastid (Sheet 2) genomes using PREPACT, PREP-suite, and REDItools, labelled by position of the edit in the coding sequence.Additional file 8: Figure S4. Number of predicted C to U editing sites in the mitochondrial and plastid genomes of E. grandis using PREPACT, PREP-suite, and REDITOOLS mRNA editing detection of polyA-selected reads. a. Number of editing sites (y-axis) in E. grandis mitochondrial genes (x-axis) as predicted by PREP-Mt (blue), PREPACT (orange), and evidence from bulked polyA-selected reads from three samples each of eight tissues in E. grandis using REDItools (DNA-RNA algorithm: minimum read depth = 10, minimum amount of reads per editing event = 3) shown in grey. b. Number of editing sites (y-axis) in E. grandis plastid genes (x-axis) as predicted by PREP-Cp (blue), PREPACT (orange), and evidence from polyA-selected reads using REDItools (grey). These figures show that bulked polyA selected reads are sufficient to detect the majority of predicted editing events in land plants, however the read depth lower than would be detected with total RNA sequencing. c. Number of predicted editing sites in common between PREP-Mt, PREPACT, and REDItools in the E. grandis mitochondrial genome. d. Number of predicted editing sites in common between PREP-Cp, PREPACT, and REDItools in the E. grandis plastid genome.Additional file 9: Table S2. Amount of E. grandis organellar DNA transfer to nuclear chromosomesAdditional file 10: Table S3. Inter-organellar DNA transfers in E. grandis show regions of high homology between E. grandis plastid and mitochondrial genomes. Additional BLAST analysis with land plant organellar genomes show that the transferred regions are all transferred from the plastid to the mitochondria (see Additional file 11).Additional file 11: Excel spreadsheet of the origin of inter-organellar DNA transfers, showing the organellar genomes of sequenced land plants, and the results of BLAST analysis of E. grandis mitochondrial genome (TAG0014_chr_M) regions that have significant homology to the E. grandis plastid genome. Note that all mitochondrial genomes analysed have no significant matches to the transferred regions, suggesting that there is no transfer of DNA from the mitochondrial genome to the plastid genome.Additional file 12: Excel spreadsheet of nuclear genes of organellar origin for mRNA-sequencing read mapping by homology using BLAST analysis (> 80% full length of gene matches with > 90% identity to organellar genome) or by annotation (annotation closest match is Arabidopsis thaliana organellar gene).Additional file 13: Figure S5. Sashimi plot of polyA-selected mRNA reads mapped to Eucgr.E01203 in E. grandis mature leaf tissue. The plot shows the count of reads (0 to 105) aligned to the annotated gene regions of Eucgr.E01203. Reads were aligned using GSNAP and visualized in the Integrated Genome Viewer. Black lines show the annotated gene regions, and thicker black bars show the annotated protein coding regions. The plot shows that the read coverage of Eucgr.E01203 across the protein coding regions is lower than in the 5’ UTR, indicating that the VST counts generated for this gene do not represent functional gene expression.Additional file 14: Table S4. Differently expressed organellar encoded genes in E. grandis where negative log2 fold change values indicate increased polyA selected RNA read abundance in mature leaf compared to immature xylem.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.en© The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License.Eucalyptus grandisOrganelle genomeMitochondriaChloroplastPlastidArticle