Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion (Q28645658)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Ancient nuclear plastid DNA in the yew family (taxaceae)

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Evidence of Selection upon Genomic GC-Content in Bacteria

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

A DNA barcode for land plants

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Biased gene conversion and the evolution of mammalian genomic landscapes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

PAML 4: phylogenetic analysis by maximum likelihood

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Chloroplast Genome (cpDNA) of Cycas taitungensis and 56 cp Protein-Coding Genes of Gnetum parvifolium: Insights into cpDNA Evolution and Phylogeny of Extant Seed Plants

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

GC-content evolution in mammalian genomes: the biased gene conversion hypothesis

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Automatic annotation of organellar genomes with DOGMA

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

THE RELATION OF RECOMBINATION TO MUTATIONAL ADVANCE

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Predominant and substoichiometric isomers of the plastid genome coexist within Juniperus plants and have shifted multiple times during cupressophyte evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

The Amborella Genome and the Evolution of Flowering Plants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Updating our view of organelle genome nucleotide landscape.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Evidence for widespread GC-biased gene conversion in eukaryotes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Evolution. Living fossil younger than thought

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Recent synchronous radiation of a living fossil

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Evidence that mutation is universally biased towards AT in bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Recombination and the maintenance of plant organelle genome stability.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Insensitivity of chloroplast gene expression to DNA methylation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Cycads: evolutionary innovations and the role of plant-derived neurotoxins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Inference of higher-order relationships in the cycads from a large chloroplast data set.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Biased gene conversion: implications for genome and sex evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Complete Sequence of the Maize Chloroplast Genome: Gene Content, Hotspots of Divergence and Fine Tuning of Genetic Information by Transcript Editing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Why do chloroplasts and mitochondria contain so many copies of their genome?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Evolutionary transfer of the chloroplast tufA gene to the nucleus.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

Compositional properties of green-plant plastid genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

Evolutionary re-organisation of a large operon in adzuki bean chloroplast DNA caused by inverted repeat movement.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

Nucleotide Substitution Rates in Legume Chloroplast DNA Depend on the Presence of the Inverted Repeat

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

Unparalleled GC content in the plastid DNA of Selaginella

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

Mitochondrial genome of the colorless green alga Polytomella capuana: a linear molecule with an unprecedented GC content

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

Unprecedented heterogeneity in the synonymous substitution rate within a plant genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

Chloroplast DNA codon use: evidence for selection at the psb A locus based on tRNA availability

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4524490

Chloroplast DNA exists in two orientations

27 November 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV125

Cytosine methylation of plastid genome in higher plants. Fact or artefact?

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26116919

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Elimination of deleterious mutations in plastid genomes by gene conversion

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26116919

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26116919

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/GBE/EVV125

1 reference

1 reference

1 reference

PubMed publication ID

26116919

1 reference