A possible breakage of linkage disequilibrium between mitochondrial and chloroplast genomes during Emmer and Dinkel wheat evolution

Genome ◽  
2013 ◽  
Vol 56 (4) ◽  
pp. 187-193 ◽  
Author(s):  
Mai Tsujimura ◽  
Naoki Mori ◽  
Hiroshi Yamagishi ◽  
Toru Terachi
Keyword(s):  
Mitochondrial Genome ◽  
Nuclear Genome ◽  
Mitochondrial Genomes ◽  
Chloroplast Microsatellite ◽  
Wheat Evolution ◽  
Closely Related Species ◽  
Genome Type ◽  
Sequence Characterized Amplified Region ◽  
Chloroplast Genomes ◽  
Different Types

In wheat (Triticum) and Aegilops, chloroplast and mitochondrial genomes have been studied for over three decades to clarify the phylogenetic relationships among species, and most of the maternal lineages of polyploid species have been clarified. Mitochondrial genomes of Emmer (tetraploid with nuclear genome AABB) and Dinkel (hexaploid with AABBDD) wheat are classified into two different types, VIIa and VIIb, by the presence–absence of the third largest HindIII fragment (named H3) in the mitochondrial DNA. Although the mitochondrial genome in the genera often provides useful information to clarify the phylogenetic relationship among closely related species, the phylogenetic significance of this dimorphism has yet not been clarified. In this study, to facilitate analysis using a large number of accessions, a sequence characterized amplified region (SCAR) marker that distinguishes the type VIIb mitochondrial genome from type VIIa was first developed. Mitochondrial genome type was determined for each of 30 accessions of wild and cultivated Emmer wheat and 25 accessions of Dinkel wheat. The mitochondrial genome type for each accession was compared with the plastogroup that had been determined using chloroplast microsatellite markers. Unexpectedly, the distribution of mitochondrial genome type was not in accordance with that of the plastogroups, suggesting occasional paternal leakage of either the mitochondrial or chloroplast genome during speciation and differentiation of Emmer and Dinkel wheat. An alternative possibility that substoichiometric shifting is involved in the observed dimorphism of the mitochondrial genome is also discussed.

scholarly journals Complete Mitochondrial Genomes of Three Mangifera Species, Their Genomic Structure And Gene Transfer From Chloroplast Genomes

2021 ◽  
Author(s):  
Yingfeng Niu ◽  
Chengwen Gao ◽  
Jin Liu
Keyword(s):  
Mitochondrial Genome ◽  
Genomic Structure ◽  
Mangifera Indica ◽  
Gene Content ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract BackgroundAmong the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species. Results Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63-69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24-27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7-10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407-6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value. ConclusionsWe sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content of Mangifera mitochondrial genomes is similar across various species. Gene transferred from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

scholarly journals Mitochondrial genomes are retained by selective constraints on protein targeting

2015 ◽  
Vol 112 (33) ◽  
pp. 10154-10161 ◽  
Author(s):  
Patrik Björkholm ◽  
Ajith Harish ◽  
Erik Hagström ◽  
Andreas M. Ernst ◽  
Siv G. E. Andersson
Keyword(s):  
Endoplasmic Reticulum ◽  
Membrane Proteins ◽  
Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Nuclear Genome ◽  
Protein Domains ◽  
Eukaryotic Cell ◽  
Mitochondrial Genomes ◽  
Hydrophobic Membrane ◽  
Selective Constraints

Mitochondria are energy-producing organelles in eukaryotic cells considered to be of bacterial origin. The mitochondrial genome has evolved under selection for minimization of gene content, yet it is not known why not all mitochondrial genes have been transferred to the nuclear genome. Here, we predict that hydrophobic membrane proteins encoded by the mitochondrial genomes would be recognized by the signal recognition particle and targeted to the endoplasmic reticulum if they were nuclear-encoded and translated in the cytoplasm. Expression of the mitochondrially encoded proteins Cytochrome oxidase subunit 1, Apocytochrome b, and ATP synthase subunit 6 in the cytoplasm of HeLa cells confirms export to the endoplasmic reticulum. To examine the extent to which the mitochondrial proteome is driven by selective constraints within the eukaryotic cell, we investigated the occurrence of mitochondrial protein domains in bacteria and eukaryotes. The accessory protein domains of the oxidative phosphorylation system are unique to mitochondria, indicating the evolution of new protein folds. Most of the identified domains in the accessory proteins of the ribosome are also found in eukaryotic proteins of other functions and locations. Overall, one-third of the protein domains identified in mitochondrial proteins are only rarely found in bacteria. We conclude that the mitochondrial genome has been maintained to ensure the correct localization of highly hydrophobic membrane proteins. Taken together, the results suggest that selective constraints on the eukaryotic cell have played a major role in modulating the evolution of the mitochondrial genome and proteome.

scholarly journals Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species Scenedesmus obliquus Strain DOE0152z

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
S. R. Starkenburg ◽  
J. E. W. Polle ◽  
B. Hovde ◽  
H. E. Daligault ◽  
K. W. Davenport ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
Green Alga ◽  
Industrial Production ◽  
Complete Mitochondrial Genome ◽  
Scenedesmus Obliquus ◽  
Nuclear Genome ◽  
Mitochondrial Genomes ◽  
Complete Chloroplast Genome ◽  
Draft Assembly

ABSTRACT The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

scholarly journals Detection of CRISPR cassettes and cas genes in the Arabidopsis thaliana genome

2019 ◽  
Vol 23 (7) ◽  
pp. 809-816
Author(s):  
Yu. M. Konstantinov ◽  
I. S. Petrushin
Keyword(s):  
Arabidopsis Thaliana ◽  
Mitochondrial Genome ◽  
Adaptive Immunity ◽  
Nuclear Genome ◽  
Plant Viruses ◽  
Cauliflower Mosaic Virus ◽  
Higher Plant ◽  
Crispr Locus ◽  
Chloroplast Genomes ◽  
Cas Genes

The state of the art in the evolution of plant viruses allows the genetic foundations of antiviral immunity in higher (including the most important crops) plants to be categorized as one of the most pressing issues of genetics and selection. According to the endosymbiotic theory, mitochondria descended from alphaproteobacteria that had been absorbed but not degraded by the host cell. The discovery of CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins), which implement the adaptive immunity function in prokaryotes, raises the question whether such a mechanism of antiviral protection could be caught up by evolution and used by representatives of eukaryotes (in particular, plants). The purpose of this work was to analyze the complete sequences of nuclear, mitochondrial, and chloroplast genomes of Arabidopsis thaliana in order to search for genetic elements similar to those in CRISPR-Cas systems of bacteria and archaea. As a result, in silico methods helped us to detect a locus of regularly intermittent short direct repeats in the mitochondrial genome of A. thaliana ecotypes. The structure of this locus corresponds to the CRISPR locus of the prokaryotic adaptive antiviral immune system. The probable connection between the locus found in the mitochondrial genome of the higher plant and the function of adaptive immunity is indicated by a similarity between the spacer sequences in the CRISPR cassette found and the genome of Cauliflower mosaic virus affecting Arabidopsis plants. Sequences of repeats and spacers of CRISPR cassettes in Arabidopsis C24 and Ler lines are perfectly identical. However, the locations of the CRISPR locus in the mitochondrial genomes of these lines differ significantly. The CRISPR cassette in the Col-0 line was found to be completely broken as a result of four deletions and one insertion. Although cas genes were not detected in the mitochondrial genome of the studied Arabidopsis ecotypes, their presence was detected in the nuclear genome. Both cas genes and numerous CRISPR cassettes were found on all the five chromosomes in the nuclear genome of the Col-0 ecotype. The results suggest the existence of a system of adaptive immunity in plants, which is similar to the CRISPR immunity of bacteria and archaea.

scholarly journals Primer designing strategy for amplification and sequencing of the complete mitochondrial genome of Semnopithecus hypoleucos

2021 ◽  
Author(s):  
Vipin Hiremath ◽  
Chandrakant Jadhav ◽  
Gulab Khedkar
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Primate Species ◽  
Mitochondrial Genomes ◽  
Evolutionary Analysis ◽  
Closely Related Species ◽  
Design And Optimization ◽  
Genome Data ◽  
Phylogenetic Studies ◽  
Conserved Gene

Abstract The mitochondrial genome is highly informative for evolutionary analysis of organism lineages and phylogenetic studies. The availability of robust primers for amplifying complete mitochondrial genomes is a crucial step in current mitogenome studies. However, organism specific characteristics such as variable transition to transversion substitution ratios seen in some groups pose challenges for the development of universal, or at least broadly applicable, primer pairs for this purpose. This study reports on a strategy of primer design and optimization (PDO) where regions of known mtDNA genescan be used for choosing primers for amplification, sequencing and assembly of entire mitochondrial genomes of several closely-related species. In brief, taking advantage of the circular organization of mtDNA, primers are first designed for amplification of “long” products using the 5’ region of one conserved gene and a 3’region from another conserved gene. Additional primers are then used to amplify “short” regions to fill in gaps to allow for complete assembly of the genome. We show how we were able to use this approach to successfully amplify entire mitochondrial genomes from a non-human primate species (Semnopithecus hypoleucos), and also how this provided data useful for annotation of the assembled genome data.

scholarly journals Mitochondrial Fostering: The Mitochondrial Genome May Play a Role in Plant Orphan Gene Evolution

2020 ◽  
Vol 11 ◽  
Author(s):  
Seth O’Conner ◽  
Ling Li
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Gene Evolution ◽  
Nuclear Genome ◽  
Bioinformatic Analysis ◽  
Land Plants ◽  
Mitochondrial Genomes ◽  
Recombination Rates ◽  
Orphan Genes ◽  
Orphan Gene

Plant mitochondrial genomes exhibit unique evolutionary patterns. They have a high rearrangement but low mutation rate, and a large size. Based on massive mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique evolutionary traits, we propose a “Mitochondrial Fostering” theory where the organelle genome plays an integral role in the arrival and development of orphan genes (genes with no homologs in other lineages). Two approaches were used to test this theory: (1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial originating DNA that migrated to the nucleus) at the genome level, and (2) bioinformatic analysis of particular orphan sequences present in both the mitochondrial genome and the nuclear genome of Arabidopsis thaliana. One study example is given about one orphan sequence that codes for two unique orphan genes: one in the mitochondrial genome and another one in the nuclear genome. DNA alignments show regions of this A. thaliana orphan sequence exist scattered throughout other land plant mitochondrial genomes. This is consistent with the high recombination rates of mitochondrial genomes in land plants. This may also enable the creation of novel coding sequences within the orphan loci, which can then be transferred to the nuclear genome and become exposed to new evolutionary pressures. Our study also reveals a high correlation between the amount of mitochondrial DNA transferred to the nuclear genome and the number of orphan genes in land plants. All the data suggests the mitochondrial genome may play a role in nuclear orphan gene evolution in land plants.

scholarly journals A model simulating the dynamics of plant mitochondrial genomes.

Genetics ◽  
1993 ◽  
Vol 135 (1) ◽  
pp. 213-222 ◽  
Author(s):  
A Atlan ◽  
D Couvet
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Evolution ◽  
Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Model Parameters ◽  
Recombination Rates ◽  
Plant Mitochondrial Genome ◽  
Cell Cycles ◽  
Different Types ◽  
Random Segregation

Abstract Molecular evolution of the plant mitochondrial genome involves rearrangements due to the presence of highly recombining repeated sequences. As a result, this genome is composed of a set of molecules of various sizes that generate each other through recombination. The model presented simulates the evolution of various frequencies of the different types of molecules over successive cell cycles. It considers the mitochondrial genome as a population of circular molecules evolving through recombination, replication and random segregation. The model parameters are the rates of recombination of each sequence, the frequency of each type of recombination, the replication rates of the circles and the total amount of mitochondrial DNA per cell. This model demonstrates that high recombination rates lead to rapid deletions of sequences in the absence of selection. The frequency of deletion is dependent on the simulated reproductive mechanism. The conditions leading to reversible or irreversible rearrangements were also investigated.

The evolution of species-type specificity in the global DNA sequence organization of mitochondrial genomes

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 342-356 ◽  
Author(s):  
Kathleen A. Hill ◽  
Shiva M. Singh
Keyword(s):  
Dna Sequence ◽  
Related Species ◽  
Nuclear Genome ◽  
Sequence Length ◽  
Mitochondrial Genomes ◽  
Evolutionary Time ◽  
Closely Related Species ◽  
Sequence Organization ◽  
Dna Sequence Organization ◽  
Species Type

Prokaryote genomes and nuclear genomes of eukaryotes have a global DNA sequence organization that is species type specific, determined primarily by nearest-neighbor nucleotide associations, and independent of gene function and sequence length. The determinants of such a global structure have remained largely uncharacterized. The monophyletic and endosymbiotic origin of mitochondria permit examination of the influence of evolutionary time and host species type. Different global structures were seen among (i) protozoan and plant, (ii) fungal, (iii) algal (iv) nematode, (v) echinoderm, (vi) insect, and (vii) vertebrate species following examination of 28 complete mitochondrial genomes using chaos representation and measures of short-sequence representation. The mitochondrial genomes have biases in single-nucleotide and dinucleotide representation, specifically, an overrepresentation of A and T nucleotides and CC/GG and AG/CT dinucleotides and a deficiency of CG dinucleotides, in all but one genome. Dinucleotide representation is similar among (i) mitochondrial genomes of more closely related species; (ii) mitochondrial genomes and the Mycoplasma capricolum genome, a proposed progenitor of mitochondrial genomes; and (iii) mitochondrial genomes of diverse species, more so than between the mitochondrial and the nuclear genome of the same or a closely related species. It is hypothesized that sufficient evolutionary time has permitted host-specific constraints to affect nuclear and mitochondrial genomes and that different species type specific constraints influence nuclear and mitochondrial genome global structure.Key words: chaos representation, mitochondrial genomes, primary sequence organization, oligonucleotide frequencies.

scholarly journals Genomic Balance: Two Genomes Establishing Synchrony to Modulate Cellular Fate and Function

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1306 ◽  
Author(s):  
St. John
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Genome ◽  
Cell Fate ◽  
Nuclear Genome ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Epigenetic Regulators ◽  
And Function ◽  
Effective Function

It is becoming increasingly apparent that cells require cooperation between the nuclear and mitochondrial genomes to promote effective function. However, it was long thought that the mitochondrial genome was under the strict control of the nuclear genome and the mitochondrial genome had little influence on cell fate unless it was extensively mutated, as in the case of the mitochondrial DNA diseases. However, as our understanding of the roles that epigenetic regulators, including DNA methylation, and metabolism play in cell fate and function, the role of the mitochondrial genome appears to have a greater influence than previously thought. In this review, I draw on examples from tumorigenesis, stem cells, and oocyte pre- and post-fertilisation events to discuss how modulating one genome affects the other and that this results in a compromise to produce functional mature cells. I propose that, during development, both of the genomes interact with each other through intermediaries to establish genomic balance and that establishing genomic balance is a key facet in determining cell fate and viability.

scholarly journals The Insights into Mitochondrial Genomes of Sunflowers

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1774
Author(s):  
Maksim S. Makarenko ◽  
Denis O. Omelchenko ◽  
Alexander V. Usatov ◽  
Vera A. Gavrilova
Keyword(s):  
Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Nuclear Genome ◽  
Jerusalem Artichoke ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Genetic Studies ◽  
Protein Coding ◽  
Significant Difference ◽  
Complete Mitochondrial Genomes

The significant difference in the mtDNA size and structure with simultaneous slow evolving genes makes the mitochondrial genome paradoxical among all three DNA carriers in the plant cell. Such features make mitochondrial genome investigations of particular interest. The genus Helianthus is a diverse taxonomic group, including at least two economically valuable species—common sunflower (H. annuus) and Jerusalem artichoke (H. tuberosus). The successful investigation of the sunflower nuclear genome provided insights into some genomics aspects and significantly intensified sunflower genetic studies. However, the investigations of organelles’ genetic information in Helianthus, especially devoted to mitochondrial genomics, are presented by limited studies. Using NGS sequencing, we assembled the complete mitochondrial genomes for H. occidentalis (281,175 bp) and H. tuberosus (281,287 bp) in the current investigation. Besides the master circle chromosome, in the case of H. tuberosus, the 1361 bp circular plasmid was identified. The mitochondrial gene content was found to be identical for both sunflower species, counting 32 protein-coding genes, 3 rRNA, 23 tRNA genes, and 18 ORFs. The comparative analysis between perennial sunflowers revealed common and polymorphic SSR and SNPs. Comparison of perennial sunflowers with H. annuus allowed us to establish similar rearrangements in mitogenomes, which have possibly been inherited from a common ancestor after the divergence of annual and perennial sunflower species. It is notable that H. occidentalis and H. tuberosus mitogenomes are much more similar to H. strumosus than H. grosseserratus.

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