Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae (Q28607097)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26416561%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

title

Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae (English)

1 reference

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25 February 2020

1 reference

1

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25 February 2020

author name string

Keenan Moukarzel

2

1 reference

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25 February 2020

Kayla N Smith

3

1 reference

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25 February 2020

Jaimin Patel

4

1 reference

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25 February 2020

Khidir W Hilu

5

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25 February 2020

language of work or name

English

0 references

publication date

29 September 2015

1 reference

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25 February 2020

published in

BMC Evolutionary Biology

1 reference

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25 February 2020

volume

15

1 reference

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25 February 2020

issue

1

0 references

page(s)

210

1 reference

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Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification

25 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Impact of gene molecular evolution on phylogenetic reconstruction: a case study in the rosids (Superorder Rosanae, Angiosperms)

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

DNA barcoding the native flowering plants and conifers of Wales

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

An organellar maturase associates with multiple group II introns

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

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=4587860

DNA barcoding the floras of biodiversity hotspots

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, 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=4587860

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis on Stanhopeinae: combined molecular evidence

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

The scanning model for translation: an update

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Multiple checkpoints for the expression of the chloroplast-encoded splicing factor MatK.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Phylogenetics of Cranichideae with emphasis on Spiranthinae (Orchidaceae, Orchidoideae): evidence from plastid and nuclear DNA sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Loss of matK RNA editing in seed plant chloroplasts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Parallel loss of plastid introns and their maturase in the genus Cuscuta

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

A frameshift mutation of the chloroplast matK coding region is associated with chlorophyll deficiency in the Cryptomeria japonica virescent mutant Wogon-Sugi

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Evaluating evolutionary constraint on the rapidly evolving gene matK using protein composition.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Tobacco chloroplast tRNA(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

A group II intron-encoded maturase functions preferentially in cis and requires both the reverse transcriptase and X domains to promote RNA splicing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Functional Shine-Dalgarno-like sequences for translational initiation of chloroplast mRNAs.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Extraordinarily high evolutionary rate of pseudogenes: evidence for the presence of selective pressure against changes between synonymous codons

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Expression of matK: functional and evolutionary implications

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step forward in understanding the evolution of the Aeridinae

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Editing of plastid RNA in Arabidopsis thaliana ecotypes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for MatK as an essential splice factor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Impaired splicing of the rps12 transcript in ribosome-deficient plastids

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Control of start codon choice on a plant viral RNA encoding overlapping genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

The chloroplast tRNALys(UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Interactive analysis of phylogeny and character evolution using the computer program MacClade.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Origin and evolution of the chloroplast trnK (matK) intron: a model for evolution of group II intron RNA structures

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

Conservation of selection on matK following an ancient loss of its flanking intron

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

Inefficient rpl2 splicing in barley mutants with ribosome-deficient plastids

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae: Epidendroideae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

Angiosperm phylogeny based on matK sequence information

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

A role for initiation codon context in chloroplast translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

A phylogenetic analysis of Apostasioideae (Orchidaceae) based on ITS, trnL-F and matK sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

Physicochemical evolution and positive selection of the gymnosperm matK proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

Evolutionary implications of matK indels in Poaceae

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

The Evolution of Non-Coding Chloroplast DNA and Its Application in Plant Systematics

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

Phylogenetic signal in matK vs. trnK: a case study in early diverging eudicots (angiosperms).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0491-1

The matK gene: sequence variation and application in plant systematics

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4587860

Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26416561

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S12862-015-0491-1

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26416561%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

25 February 2020

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/s12862-015-0491-1

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26416561%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

PubMed publication ID

26416561

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26416561%20AND%20SRC:MED&resulttype=core&format=json