(Q34460412)

English

Exploring the limits for reduction of plastid genomes: a case study of the mycoheterotrophic orchids Epipogium aphyllum and Epipogium roseum.

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scholarly article

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Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635040%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

Exploring the limits for reduction of plastid genomes: a case study of the mycoheterotrophic orchids Epipogium aphyllum and Epipogium roseum (English)

1 reference

Europe PubMed Central

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29 February 2020

Myco-heterotrophy

1 reference

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Epipogium aphyllum

object named as

Epipogium aphyllum

1 reference

based on heuristic

inferred from title

Mikhail I. Schelkunov

1

1 reference

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29 February 2020

Victoria Shtratnikova

2

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29 February 2020

Maxim S Nuraliev

3

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29 February 2020

5

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29 February 2020

Marc-André Selosse

4

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Marc-Andre Selosse

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29 February 2020

author name string

Maria D Logacheva

6

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29 February 2020

publication date

28 January 2015

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29 February 2020

Genome Biology and Evolution

1 reference

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29 February 2020

7

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29 February 2020

4

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29 February 2020

1179-1191

1 reference

Europe PubMed Central

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29 February 2020

Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Selecting optimal partitioning schemes for phylogenomic datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Trimmomatic: a flexible trimmer for Illumina sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

The translational apparatus of plastids and its role in plant development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

A plastid without a genome: evidence from the nonphotosynthetic green algal genus Polytomella.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

tRNA anticodon shifts in eukaryotic genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

The plastid genome of mycoheterotrophic monocot Petrosavia stellaris exhibits both gene losses and multiple rearrangements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Parasitic plants have increased rates of molecular evolution across all three genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Versatile roles of Arabidopsis plastid ribosomal proteins in plant growth and development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Extreme genome reduction in symbiotic bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Sequencing and analysis of plastid genome in mycoheterotrophic orchid Neottia nidus-avis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Correlation between nuclear plastid DNA abundance and plastid number supports the limited transfer window hypothesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA results

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

The evolution of parasitism in plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Saprotrophic fungal mycorrhizal symbionts in achlorophyllous orchids: finding treasures among the 'molecular scraps'?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Ectomycorrhizal Inocybe species associate with the mycoheterotrophic orchid Epipogium aphyllum but not its asexual propagules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Functional Gene Losses Occur with Minimal Size Reduction in the Plastid Genome of the Parasitic Liverwort Aneura mirabilis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

PAML 4: phylogenetic analysis by maximum likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

The genomic rate of adaptive evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Why are plastid genomes retained in non-photosynthetic organisms?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae): Comparative Analysis of Evolutionary Rate with that of Grasses and Its Phylogenetic Implications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

VISTA: computational tools for comparative genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Automatic annotation of organellar genomes with DOGMA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

NONPHOTOSYNTHETIC METABOLISM IN PLASTIDS.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Maize BMS cultured cell lines survive with massive plastid gene loss

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Direct measurement of the transfer rate of chloroplast DNA into the nucleus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Gravitropism in higher plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Reducing the genome size of organelles favours gene transfer to the nucleus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Multi-functional acetyl-CoA carboxylase from Brassica napus is encoded by a multi-gene family: indication for plastidic localization of at least one isoform

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Editing corrects mispairing in the acceptor stem of bean and potato mitochondrial phenylalanine transfer RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Comparative organization of chloroplast genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Anticodon and acceptor stem nucleotides in tRNAGln are major recognition elements for E. coli glutaminyl-tRNA synthetase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4419786

6 July 2018

Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

The chloroplast genome of a Symbiodinium sp. clade C3 isolate

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

The plastid clpP gene may not be essential for plant cell viability

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

Utility of plastid psaB gene sequences for investigating intrafamilial relationships within Orchidaceae

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

GenomeVx: simple web-based creation of editable circular chromosome maps.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

Nonessential plastid-encoded ribosomal proteins in tobacco: a developmental role for plastid translation and implications for reductive genome evolution.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

The plastid clpP1 protease gene is essential for plant development.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

Stable isotope signatures confirm carbon and nitrogen gain through ectomycorrhizas in the ghost orchid Epipogium aphyllum Swartz

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

The causes of mutation accumulation in mitochondrial genomes

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

Potential functional replacement of the plastidic acetyl-CoA carboxylase subunit (accD) gene by recent transfers to the nucleus in some angiosperm lineages.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

Single gene circles in dinoflagellate chloroplast genomes.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV019

21 January 2018

Multiple and different genomic rearrangements of the rbcL gene are present in the parasitic orchid Neottia nidus-avis

1 reference

https://pubmed.ncbi.nlm.nih.gov/25635040

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/25635040

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Deleterious mutation accumulation in organelle genomes

1 reference

https://pubmed.ncbi.nlm.nih.gov/25635040

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stable albinism induced without mutagenesis: a model for ribosome-free plastid inheritance

1 reference

https://pubmed.ncbi.nlm.nih.gov/25635040

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/GBE/EVV019

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635040%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635040%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635040%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

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