(Q46531338)

22 December 2017

title

The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes (English)

1 reference

22 December 2017

author

Justin C Havird

series ordinal

1

1 reference

22 December 2017

author name string

Daniel B Sloan

series ordinal

2

1 reference

22 December 2017

publication date

25 August 2016

1 reference

22 December 2017

Molecular Biology and Evolution

published in

1 reference

22 December 2017

volume

33

1 reference

22 December 2017

issue

12

1 reference

22 December 2017

page(s)

3042-3053

1 reference

22 December 2017

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress.

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The Roles of Compensatory Evolution and Constraint in Aminoacyl tRNA Synthetase Evolution

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Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression

24 May 2018

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Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism

24 May 2018

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Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes

24 May 2018

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Implications of mutation of organelle genomes for organelle function and evolution

24 May 2018

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Determinants of the rate of protein sequence evolution

24 May 2018

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Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes

24 May 2018

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Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

24 May 2018

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Cytonuclear evolution of rubisco in four allopolyploid lineages

24 May 2018

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Genes and junk in plant mitochondria-repair mechanisms and selection

24 May 2018

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Chromera velia, endosymbioses and the rhodoplex hypothesis--plastid evolution in cryptophytes, alveolates, stramenopiles, and haptophytes (CASH lineages)

24 May 2018

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Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes

24 May 2018

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Evolutionary perspectives on the links between mitochondrial genotype and disease phenotype.

24 May 2018

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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes?

24 May 2018

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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Mitonuclear protein imbalance as a conserved longevity mechanism

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

An Incompatibility between a mitochondrial tRNA and its nuclear-encoded tRNA synthetase compromises development and fitness in Drosophila

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

The effects of mitochondrial genotype on hypoxic survival and gene expression in a hybrid population of the killifish, Fundulus heteroclitus

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Aligning short sequencing reads with Bowtie

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Diversity and reductive evolution of mitochondria among microbial eukaryotes

24 May 2018

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Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Why chloroplasts and mitochondria contain genomes

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

A mitochondrial protein compendium elucidates complex I disease biology

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

A genome-wide view of the spectrum of spontaneous mutations in yeast.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Coordination of gene expression between organellar and nuclear genomes

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Uncovering the mutation-fixation correlation in short lineages

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants.

24 May 2018

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PAML 4: phylogenetic analysis by maximum likelihood

24 May 2018

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Locating proteins in the cell using TargetP, SignalP and related tools

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Intergenomic epistasis for fitness: within-population interactions between cytoplasmic and nuclear genes in Drosophila melanogaster

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Hearing silence: non-neutral evolution at synonymous sites in mammals

24 May 2018

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Molecular signatures of natural selection

24 May 2018

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24 May 2018

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

24 May 2018

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Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes

24 May 2018

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24 May 2018

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Evolution of mitochondrial gene content: gene loss and transfer to the nucleus

24 May 2018

1 reference

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24 May 2018

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Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution

24 May 2018

1 reference

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Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes

24 May 2018

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Animal mitochondrial genomes

24 May 2018

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The mitochondrial genome: structure, transcription, translation and replication

24 May 2018

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24 May 2018

Mitochondrial evolution

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The role of protein degradation in mitochondrial function and biogenesis.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Expression of a recoded nuclear gene inserted into yeast mitochondrial DNA is limited by mRNA-specific translational activation.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Glucose repression of yeast mitochondrial transcription: kinetics of derepression and role of nuclear genes

24 May 2018

1 reference

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Stoichiometry of mitochondrial transcripts and regulation of gene expression by mitochondrial transcription factor A.

24 May 2018

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Mitochondrial DNA sequences of primates: Tempo and mode of evolution

24 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Synthesis and turnover rates of four rat liver mitochondrial RNA species.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Rapid evolution of animal mitochondrial DNA

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Changes in DNA damage, molecular integrity, and copy number for plastid DNA and mitochondrial DNA during maize development

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Evidence for compensatory evolution of ribosomal proteins in response to rapid divergence of mitochondrial rRNA.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Key transitions in animal evolution: a mitochondrial DNA perspective.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

The sorry state of F2 hybrids: consequences of rapid mitochondrial DNA evolution in allopatric populations

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Coordination of nuclear and mitochondrial genome expression during mitochondrial biogenesis in Arabidopsis

15 August 2018

1 reference

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The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants

15 August 2018

1 reference

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Dual roles of photosynthetic electron transport in photosystem I biogenesis: light induction of mRNAs and chromatic regulation at post-mRNA level

15 August 2018

1 reference

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High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Oxidative stress and aging reduce COX I RNA and cytochrome oxidase activity in Drosophila.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

The causes of mutation accumulation in mitochondrial genomes

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5100045

Purifying Selection in Mammalian Mitochondrial Protein-Coding Genes Is Highly Effective and Congruent with Evolution of Nuclear Genes

29 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW185

The Positive Correlation between dN/dS and dS in Mammals Is Due to Runs of Adjacent Substitutions

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW185

Deleterious mutation accumulation in organelle genomes

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27563053

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Messenger RNA for ribosomal proteins in yeast

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27563053

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27563053

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSW185

1 reference

22 December 2017

PMC publication ID

5100045

1 reference

22 December 2017

PubMed publication ID

27563053

1 reference

22 December 2017