dc.contributor.author |
Pinard, Desre
|
|
dc.contributor.author |
Myburg, Alexander Andrew
|
|
dc.contributor.author |
Mizrachi, Eshchar
|
|
dc.date.accessioned |
2020-07-11T07:02:06Z |
|
dc.date.available |
2020-07-11T07:02:06Z |
|
dc.date.issued |
2019-02-13 |
|
dc.description |
Additional file 1: Table S1. E. grandis mitochondrial and plastid
genome short repeat elements overview |
en_ZA |
dc.description |
Additional 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. |
en_ZA |
dc.description |
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). |
en_ZA |
dc.description |
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. |
en_ZA |
dc.description |
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. |
en_ZA |
dc.description |
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. |
en_ZA |
dc.description |
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. |
en_ZA |
dc.description |
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. |
en_ZA |
dc.description |
Additional file 9: Table S2. Amount of E. grandis organellar DNA
transfer to nuclear chromosomes |
en_ZA |
dc.description |
Additional 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). |
en_ZA |
dc.description |
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. |
en_ZA |
dc.description |
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). |
en_ZA |
dc.description |
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. |
en_ZA |
dc.description |
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. |
en_ZA |
dc.description.abstract |
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_ZA |
dc.description.department |
Biochemistry |
en_ZA |
dc.description.department |
Forestry and Agricultural Biotechnology Institute (FABI) |
en_ZA |
dc.description.department |
Genetics |
en_ZA |
dc.description.department |
Microbiology and Plant Pathology |
en_ZA |
dc.description.librarian |
am2020 |
en_ZA |
dc.description.sponsorship |
The Department of Science and Technology
(Strategic Grant for the Eucalyptus Genomics Platform) and National
Research Foundation of South Africa (Bioinformatics and Functional
Genomics Programme, Grants 86936 and 97911 to A.A.M.), Sappi South
Africa, the Technology and Human Resources for Industry Programme (Grant
80118) through the Forest Molecular Genetics Programme at the University
of Pretoria (to A.A.M.), and D.P. is supported by the National Research
Foundation of South Africa Scarce Skills grant. |
en_ZA |
dc.description.uri |
https://bmcgenomics.biomedcentral.com |
en_ZA |
dc.identifier.citation |
Pinard, D., Myburg, A.A. & Mizrachi, E. 2019, 'The plastid and mitochondrial genomes of
Eucalyptus grandis', BMC Genomics, vol. 20, art. 132, pp. 1-14. |
en_ZA |
dc.identifier.issn |
1471-2164 (online) |
|
dc.identifier.other |
10.1186/s12864-019-5444-4 |
|
dc.identifier.uri |
http://hdl.handle.net/2263/75145 |
|
dc.language.iso |
en |
en_ZA |
dc.publisher |
BioMed Central |
en_ZA |
dc.rights |
© The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License. |
en_ZA |
dc.subject |
Eucalyptus grandis |
en_ZA |
dc.subject |
Organelle genome |
en_ZA |
dc.subject |
Mitochondria |
en_ZA |
dc.subject |
Chloroplast |
en_ZA |
dc.subject |
Plastid |
en_ZA |
dc.title |
The plastid and mitochondrial genomes of Eucalyptus grandis |
en_ZA |
dc.type |
Article |
en_ZA |