Analysis of nuclear mitochondrial DNAs and factors affecting patterns of integration in plant species

Yoshida, Takanori; Furihata, Hazuka Y.; Kawabe, Akira

doi:10.1266/ggs.16-00039

Cited by 12 publications

(13 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The nuclear integrants of organellar DNA were first discovered in a study in which a mitochondrial ATPase subunit gene was found in the nuclear genome, as well as in the mitochondrial genome of Neurospora crassa [25]. Since then, organelle-derived sequences were examined in the nuclear genome of a number of animals [26][27][28][29][30][31][32] and plants [15][16][17][18][19][20][21]. The availability of a large amount of plant organelle and nuclear genome data has made it possible to investigate the prevalence and characteristics of NUMTs and NUPTs in plants.…”

Section: Characterization Of Organellar Dna-derived Sequences In Plantsmentioning

confidence: 99%

See 1 more Smart Citation

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

Zhang

Dong

Lan

et al. 2020

IJMS

View full text Add to dashboard Cite

The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.

show abstract

Section: Characterization Of Organellar Dna-derived Sequences In Plantsmentioning

confidence: 99%

“…This makes the large-scale analysis of NUPTs and NUMTs in plants be possible. Currently, NUPTs and NUMTs in some plant genomes have been characterized [15][16][17][18][19][20][21]. The characterization of nuclear organellar DNAs in plants adds new insights into the role of NUPTs and NUMTs in genome structure and evolution.…”

Section: Introductionmentioning

confidence: 99%

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

Zhang

Dong

Lan

et al. 2020

IJMS

View full text Add to dashboard Cite

show abstract

“…Thus, the most important result seems to be the potential use of animal signal sequences for heterologous gene expression in plant cells, which will allow to evaluate the ancient endosymbiotic event results in a new light (Perry et al, 2006;Yoshida et al, 2017). Until now, this opportunity was clearly demonstrated only in studies performed solely in vitro (Luzikov et al, 1994).…”

Section: Discussionmentioning

confidence: 99%

Targeted Protection of Mitochondria of Mesophyll Cells in Transgenic CYP11A1 CDNA Expressing Tobacco Plant Leaves After NaCl-Induced Stress Damage

Баранова

Khaliluev

Спивак

et al. 2018

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences.

View full text Add to dashboard Cite

Recently we have showed that the expression of the mammalian CYP11A1 cDNA in plants confers their resistance to abiotic and biotic stresses. To determine the role of heterologous expression of cytochrome P450scc cDNA in resistance to ROS (radical oxygen species) dependent abiotic stresses, the structural changes of mitochondria and peroxisomes were studied under 150 mM NaCl-induced 14-day salinity treatment on juvenile tobacco plants in in vitro culture. Ultrastructural analysis of mesophyll cells of transgenic tobacco leaves constitutively expressing CYP11A1 cDNA was performed. Under NaCl stress, a change in shape from rounded to elon-gated, reduced section area, formation of branched mitochondria, as well as the emergence of triangular and rhomboid cristae, densification of a mitochondrial matrix, increase in density of contrasting membranes and their thickness were observed in non-transgenic plants. Transgenic plants without stress applied had mitochondria with rounded and elongated shape, twice as small as in non-transgenic plants, with a dense matrix and sinuous cristae. Surprisingly, the effect of NaCl led to increase in size of mitochondria by 1.5 times, decomposition of matrix and the emergence in organelles of light zones presumably containing mitochondrial DNA strands. Thus, the structural organisation of transgenic plant mitochondria under salinity treatment was comparable to that of non-transgenic plants under native conditions. It was also noted that the transgenic plant peroxisomes differed in non-transgenic tobacco both in normal condition and under the action of NaCl. The observed differences in ultrastructural organisation of mitochondria not only support our earlier notion about successful incorporation of the mature P450scc into this organelle, but for the first time demonstrate that the mammalian CYP11A1 signal peptide sequence could be efficiently used in the formation of targeted mitochondria protection of plants from salinity-induced damage.

show abstract

“…The gene content and genome complexity of nuclear genomes differs among angiosperm taxa typically associated with these continuing intercompartmental DNA transfer events [12]. In contrast to those beneficial or nonfunctional long-existing nuclear organelle integrations, substantial numbers of newly formed norgDNA are more deleterious and are rapidly eliminated [14,15]. The pattern and mechanism of organelle-to-nucleus DNA transfer has been analyzed in detail in a number of species [16,17].…”

Section: Introductionmentioning

confidence: 99%

Genomic Variation between PRSV Resistant Transgenic SunUp and Its Progenitor Cultivar Sunset

Fang

Wood

Chen

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. Results: In this study, a total of more than 74 million Illumina reads for progenitor ‘Sunset’ were mapped onto transgenic papaya ‘SunUp’ reference genome. 310,364 single nucleotide polymorphisms (SNPs), 34,071 small Inserts/deletions (InDels) and 1,200 large structural variations (SVs) were detected between ‘Sunset’ and ‘SunUp’. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4×10-4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. Spontaneous mutations were the leading cause of SNPs in transgenic papaya ‘SunUp’. A total of 3,430 nuclear plastid DNA (NUPT) and 2,764 nuclear mitochondrial DNA (NUMT) junction sites have been found in ‘SunUp’, which is proportionally higher than the predicted total NUPT and NUMT junction sites in ‘Sunset’ (3,346 and 2,745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by ‘SunUp’ and ‘Sunset’. The average identity between ‘SunUp’ specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by ‘SunUp’ and ‘Sunset’. Six ‘SunUp’ organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18~100%). None of the paired-end spans of mapped ‘Sunset’ reads were elongated by any ‘SunUp’ transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions.Conclusions: Comparative whole-genome analyses between ‘SunUp’ and ‘Sunset’ provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.

show abstract

Analysis of nuclear mitochondrial DNAs and factors affecting patterns of integration in plant species

Cited by 12 publications

References 42 publications

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

Targeted Protection of Mitochondria of Mesophyll Cells in Transgenic CYP11A1 CDNA Expressing Tobacco Plant Leaves After NaCl-Induced Stress Damage

Genomic Variation between PRSV Resistant Transgenic SunUp and Its Progenitor Cultivar Sunset

Contact Info

Product

Resources

About