(Q90581357)

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Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat

scientific article published on 24 January 2019

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scholarly article

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14 April 2020

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat (English)

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14 April 2020

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Jeffrey P Mower

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14 April 2020

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14 April 2020

Robert VanBuren

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14 April 2020

author name string

Peng-Fei Ma

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14 April 2020

Felix Grewe

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14 April 2020

Alex Taylor

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14 April 2020

Yin-Long Qiu

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14 April 2020

publication date

24 January 2019

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14 April 2020

New Phytologist

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14 April 2020

222

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14 April 2020

2

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14 April 2020

1061-1075

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14 April 2020

Structural rearrangements of the chloroplast genome provide an important phylogenetic link in ferns

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dispersed repeats and structural reorganization in subclover chloroplast DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RNA editing in bryophytes and a molecular phylogeny of land plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

MODELTEST: testing the model of DNA substitution

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The phylogenetic history of Selaginellaceae based on DNA sequences from the plastid and nucleus: extreme substitution rates and rate heterogeneity.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Circular chloroplast chromosomes: the grand illusion

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

HyPhy: hypothesis testing using phylogenies

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae).

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Complete Chloroplast Genome Sequence of Pelargonium x hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Gene Relocations within Chloroplast Genomes of Jasminum and Menodora (Oleaceae) Are Due to Multiple, Overlapping Inversions

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta)

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Unparalleled GC content in the plastid DNA of Selaginella

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An organellar maturase associates with multiple group II introns

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae).

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The mitochondrial genome of the lycophyte Huperzia squarrosa: the most archaic form in vascular plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The chloroplast genome of Pellia endiviifolia: gene content, RNA-editing pattern, and the origin of chloroplast editing

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evolution of plant mitochondrial intron-encoded maturases: frequent lineage-specific loss and recurrent intracellular transfer to the nucleus

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Organellar genomes of the four-toothed moss, Tetraphis pellucida.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The dynamic history of plastid genomes in the Campanulaceae sensu lato is unique among angiosperms

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Complete chloroplast genome of a valuable medicinal plant, Huperzia serrata (Lycopodiaceae), and comparison with its congener.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

GeSeq - versatile and accurate annotation of organelle genomes

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The timescale of early land plant evolution.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A novel chloroplast gene reported for flagellate plants.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mobile Elements Shape Plastome Evolution in Ferns

1 reference

https://pubmed.ncbi.nlm.nih.gov/30556907

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1111/NPH.15650

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30556907%20AND%20SRC:MED&resulttype=core&format=json

14 April 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30556907%20AND%20SRC:MED&resulttype=core&format=json

14 April 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30556907%20AND%20SRC:MED&resulttype=core&format=json

14 April 2020

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