Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae (Q34304593)

25270575

1 August 2017

title

Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae (English)

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1 August 2017

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1

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4 June 2020

Monique Turmel

series ordinal

3

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4 June 2020

author name string

Christian Otis

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2

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4 June 2020

publication date

1 October 2014

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25270575

1 August 2017

published in

BMC Evolutionary Biology

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4 June 2020

volume

14

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4 June 2020

page(s)

211

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Creative Commons Attribution 4.0 International

4 June 2020

copyright license

start time

1 October 2014

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April 2022 Public Data File from Crossref

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copyrighted

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cites work

ANALYSIS OF A PLASTID MULTIGENE DATA SET AND THE PHYLOGENETIC POSITION OF THE MARINE MACROALGA CAULERPA FILIFORMIS (CHLOROPHYTA)(1).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

SSU rRNA GENE PHYLOGENY OF MORPHOSPECIES AFFILIATED TO THE BIOASSAY ALGA "SELENASTRUM CAPRICORNUTUM" RECOVERED THE POLYPHYLETIC ORIGIN OF CRESCENT-SHAPED CHLOROPHYTA(1).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

MOLECULAR PHYLOGENY OF ANTARCTIC PRASIOLA (PRASIOLALES, TREBOUXIOPHYCEAE) REVEALS EXTENSIVE CRYPTIC DIVERSITY(1).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Classification of crucigenoid algae: phylogenetic position of the reinstated genus Lemmermannia, Tetrastrum spp. Crucigenia tetrapedia, and C. lauterbornii (Trebouxiophyceae, Chlorophyta)(1).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Morphology and Phylogenetic Position of the Freshwater Green Microalgae Chlorochytrium (Chlorophyceae) and Scotinosphaera (Scotinosphaerales, ord. nov., Ulvophyceae).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Putting incertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Inclusion of chloroplast genes that have undergone expansion misleads phylogenetic reconstruction in the Chlorophyta

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Tracing the evolution of streptophyte algae and their mitochondrial genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Desiccation stress and tolerance in green algae: consequences for ultrastructure, physiological and molecular mechanisms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two novel Chlorella-like green microalgae (Trebouxiophyceae, Chlorophyta) from subaerial habitats.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Nested in the Chlorellales or Independent Class? Phylogeny and Classification of the Pedinophyceae (Viridiplantae) Revealed by Molecular Phylogenetic Analyses of Complete Nuclear and Plastid-encoded rRNA Operons

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Biofuels from algae: challenges and potential

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Green algae and the origin of land plants

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Resolving difficult phylogenetic questions: why more sequences are not enough

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

The Bryopsis hypnoides plastid genome: multimeric forms and complete nucleotide sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Acoelomorph flatworms are deuterostomes related to Xenoturbella

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

The systematics of Zoochlorella revisited employing an integrative approach

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

The exceptionally large chloroplast genome of the green alga Floydiella terrestris illuminates the evolutionary history of the Chlorophyceae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Evolution and cytological diversification of the green seaweeds (Ulvophyceae).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

The Chloroplast Genomes of the Green Algae Pyramimonas, Monomastix, and Pycnococcus Shed New light on the Evolutionary History of Prasinophytes and the Origin of the Secondary Chloroplasts of Euglenids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

A site- and time-heterogeneous model of amino acid replacement.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

RNAmmer: consistent and rapid annotation of ribosomal RNA genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Genome sequencing in microfabricated high-density picolitre reactors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

The Chloroplast Genome Sequence of the Green Alga Pseudendoclonium akinetum (Ulvophyceae) Reveals Unusual Structural Features and New Insights into the Branching Order of Chlorophyte Lineages

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Phylogeny of the non-photosynthetic green micro-algal genus Prototheca (Trebouxiophyceae, Chlorophyta) and related taxa inferred from SSU and LSU ribosomal DNA partial sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

An approximately unbiased test of phylogenetic tree selection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

CONSEL: for assessing the confidence of phylogenetic tree selection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

EMBOSS: the European Molecular Biology Open Software Suite

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Consed: a graphical tool for sequence finishing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

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

6 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

6 July 2018

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

Flagellar apparatus absolute orientations and the phylogeny of the green algae

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Comparative and functional anatomy of group II catalytic introns—a review

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4189289

Phylogeny and Molecular Evolution of the Green Algae

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

Generic concept in Chlorella-related coccoid green algae (Chlorophyta, Trebouxiophyceae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

Large-scale sequencing and the new animal phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

The Green Algal Ancestry of Land Plants as Revealed by the Chloroplast Genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

DEEP DIVISION IN THE CHLOROPHYCEAE (CHLOROPHYTA) REVEALED BY CHLOROPLAST PHYLOGENOMIC ANALYSES(1).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

INFERRING TAXONOMIC POSITIONS AND TESTING GENUS LEVEL ASSIGNMENTS IN COCCOID GREEN LICHEN ALGAE: A PHYLOGENETIC ANALYSIS OF 18S RIBOSOMAL RNA SEQUENCES FROM DICTYOCHLOROPSIS RETICULATA AND FROM MEMBERS OF THE GENUS MYRMECIA (CHLOROPHYTA, TREBOUXIOPHY

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

Symbiotic lifestyle and phylogenetic relationships of the bionts of Mastodia tessellata (Ascomycota, incertae sedis).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

Microalgae for biodiesel production and other applications: A review

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

ASSESSING PHYLOGENETIC AFFINITIES AND SPECIES DELIMITATIONS IN KLEBSORMIDIALES (STREPTOPHYTA): NUCLEAR-ENCODED rDNA PHYLOGENIES AND ITS SECONDARY STRUCTURE MODELS IN KLEBSORMIDIUM, HORMIDIELLA, AND ENTRANSIA(1).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

A 20-state empirical amino-acid substitution model for green plant chloroplasts

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

Modeling protein evolution with several amino acid replacement matrices depending on site rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12862-014-0211-2

10.1186/S12862-014-0211-2

21 January 2018

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