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Chloroplast Phylogenomic Inference of Green Algae Relationships

https://doi.org/10.1038/srep20528

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bies.201100035openalex-snapshot

Into the deep: New discoveries at the base of the green plant phylogeny

inferredcites →https://doi.org/10.1007/s00239-010-9398-zopenalex-snapshot

Automated Removal of Noisy Data in Phylogenomic Analyses

inferredcites →https://doi.org/10.1016/0014-5793(92)81231-aopenalex-snapshot

Controversy on chloroplast origins

inferredcites →https://doi.org/10.1016/j.mbs.2003.10.004openalex-snapshot

A phase transition for a random cluster model on phylogenetic trees

inferredcites →https://doi.org/10.1016/j.protis.2011.11.004openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.tig.2006.02.003openalex-snapshot

Phylogenomics: the beginning of incongruence?

inferredcites →https://doi.org/10.1016/j.tplants.2013.04.009openalex-snapshot

Origin of land plants using the multispecies coalescent model

inferredcites →https://doi.org/10.1016/j.tplants.2014.06.006openalex-snapshot

Overly simplistic substitution models obscure green plant phylogeny

inferredcites →https://doi.org/10.1046/j.1529-8817.1998.340312.xopenalex-snapshot

ORIGINS AND AFFINITIES OF THE FILAMENTOUS GREEN ALGAL ORDERS CHAETOPHORALES AND OEDOGONIALES BASED ON 18S rRNA GENE SEQUENCES

inferredcites →https://doi.org/10.1046/j.1529-8817.2001.01004.xopenalex-snapshot

TRADITIONAL GENERIC CONCEPTS VERSUS 18S rRNA GENE PHYLOGENY IN THE GREEN ALGAL FAMILY SELENASTRACEAE (CHLOROPHYCEAE, CHLOROPHYTA)

inferredcites →https://doi.org/10.1073/pnas.0709121104openalex-snapshot

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

inferredcites →https://doi.org/10.1073/pnas.0907801107openalex-snapshot

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot

Phylotranscriptomic analysis of the origin and early diversification of land plants

inferredcites →https://doi.org/10.1073/pnas.1420858112openalex-snapshot

The two-domain tree of life is linked to a new root for the Archaea

inferredcites →https://doi.org/10.1073/pnas.84.1.166openalex-snapshot

The guanine and cytosine content of genomic DNA and bacterial evolution.

inferredcites →https://doi.org/10.1073/pnas.85.8.2653openalex-snapshot

Directional mutation pressure and neutral molecular evolution.

inferredcites →https://doi.org/10.1080/07352689.2011.615705openalex-snapshot

Phylogeny and Molecular Evolution of the Green Algae

inferredcites →https://doi.org/10.1080/09670262.2013.768357openalex-snapshot

Tetraselmis indica(Chlorodendrophyceae, Chlorophyta), a new species isolated from salt pans in Goa, India

inferredcites →https://doi.org/10.1093/bioinformatics/btp368openalex-snapshot

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

inferredcites →https://doi.org/10.1093/gbe/evr080openalex-snapshot

Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit

inferredcites →https://doi.org/10.1093/gbe/evr095openalex-snapshot

Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

inferredcites →https://doi.org/10.1093/gbe/evr105openalex-snapshot

Systematic Error in Seed Plant Phylogenomics

inferredcites →https://doi.org/10.1093/gbe/evt135openalex-snapshot

Tracing the Evolution of Streptophyte Algae and Their Mitochondrial Genome

inferredcites →https://doi.org/10.1093/molbev/msi182openalex-snapshot

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

inferredcites →https://doi.org/10.1093/molbev/msp138openalex-snapshot

The Chloroplast Genomes of the Green Algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria Reveal a Shared Ancestry between the Pedinomonadales and Chlorellales

inferredcites →https://doi.org/10.1093/molbev/msq091openalex-snapshot

Evolution and Cytological Diversification of the Green Seaweeds (Ulvophyceae)

inferredcites →https://doi.org/10.1093/molbev/msq097openalex-snapshot

Compositional Heterogeneity and Phylogenomic Inference of Metazoan Relationships

inferredcites →https://doi.org/10.1093/molbev/msr121openalex-snapshot

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

inferredcites →https://doi.org/10.1093/molbev/mst200openalex-snapshot

Streptophyte Algae and the Origin of Land Plants Revisited Using Heterogeneous Models with Three New Algal Chloroplast Genomes

inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot

MUSCLE: multiple sequence alignment with high accuracy and high throughput

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

inferredcites →https://doi.org/10.1093/sysbio/syr064openalex-snapshot

A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases

inferredcites →https://doi.org/10.1093/sysbio/sys070openalex-snapshot

The Evolutionary Root of Flowering Plants

inferredcites →https://doi.org/10.1093/sysbio/syt068openalex-snapshot

Posterior Predictive Bayesian Phylogenetic Model Selection

inferredcites →https://doi.org/10.1093/sysbio/syu049openalex-snapshot

Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias

inferredcites →https://doi.org/10.1093/sysbio/syu132openalex-snapshot

Phycas: Software for Bayesian Phylogenetic Analysis

inferredcites →https://doi.org/10.1098/rstb.2007.2236openalex-snapshot

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

inferredcites →https://doi.org/10.1099/ijs.0.02256-0openalex-snapshot

Phylogenetic affinities of the Trentepohliales inferred from small-subunit rDNA

inferredcites →https://doi.org/10.1111/j.0022-3646.1994.00500.xopenalex-snapshot

ASSESSING THE RELATIONSHIPS OF SOME COCCOID GREEN LICHEN ALGAE AND THE MICROTHAMNIALES (CHLOROPHYTA) WITH 18S RIBOSOMAL RNA GENE SEQUENCE COMPARISONS1

inferredcites →https://doi.org/10.1111/j.1096-0031.1985.tb00431.xopenalex-snapshot

TRANSITION TO A LAND FLORA: PHYLOGENETIC RELATIONSHIPS OF THE GREEN ALGAE AND BRYOPHYTES

inferredcites →https://doi.org/10.1111/j.1475-4983.2011.01054.xopenalex-snapshot

Proterozoic phytoplankton and timing of Chlorophyte algae origins

inferredcites →https://doi.org/10.1111/jpy.12021openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1471-2148-12-100openalex-snapshot

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

inferredcites →https://doi.org/10.1186/1471-2148-4-35openalex-snapshot

Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?

inferredcites →https://doi.org/10.1186/1471-2164-15-857openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s12862-014-0211-2openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s12864-015-1418-3openalex-snapshot

The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin

inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

inferredcites →https://doi.org/10.1371/journal.pone.0121020openalex-snapshot

The Complete Chloroplast and Mitochondrial Genomes of the Green Macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta)

inferredcites →https://doi.org/10.2307/2399900openalex-snapshot

Phylogenetic Relationships of the "Green Algae" and "Bryophytes"

inferredcites →https://doi.org/10.2307/2992396openalex-snapshot

A Framework for the Quantitative Study of Evolutionary Trees

inferredcites →https://doi.org/10.3389/fevo.2014.00063openalex-snapshot

New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data

inferredcites →https://doi.org/10.3732/ajb.1200584openalex-snapshot

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

inferredcites →https://doi.org/10.3732/ajb.91.10.1535openalex-snapshot

Green algae and the origin of land plants

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Pitfalls in supermatrix phylogenomics

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Algae from Primary Endosymbioses

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inferred← citeshttps://doi.org/10.1007/s00606-017-1436-5openalex-snapshot

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Plastid genomes of Elaeagnus mollis: comparative and phylogenetic analyses

inferred← citeshttps://doi.org/10.1007/s42995-024-00242-0openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/b978-0-12-821477-0.00020-9openalex-snapshot

Integrated omics perspective to understand the production of high-value added biomolecules (HVABs) in microalgal cell factories

inferred← citeshttps://doi.org/10.1016/bs.abr.2017.11.010openalex-snapshot

Evolution of the Plastid Genome in Green Algae

inferred← citeshttps://doi.org/10.1016/bs.abr.2017.11.012openalex-snapshot

Comparative Plastid Genomics of Glaucophytes

inferred← citeshttps://doi.org/10.1016/j.algal.2017.04.008openalex-snapshot

A new insight into cell walls of Chlorophyta

inferred← citeshttps://doi.org/10.1016/j.algal.2018.09.012openalex-snapshot

Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)

inferred← citeshttps://doi.org/10.1016/j.cub.2016.11.056openalex-snapshot

An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids

inferred← citeshttps://doi.org/10.1016/j.gene.2023.147287openalex-snapshot

Seven newly sequenced chloroplast genomes from the order Watanabeales (Trebouxiophyceae, Chlorophyta): Phylogenetic and comparative analysis

inferred← citeshttps://doi.org/10.1016/j.margen.2020.100752openalex-snapshot

The chloroplast genome sequence of the green macroalga Caulerpa okamurae (Ulvophyceae, Chlorophyta): Its structural features, organization and phylogenetic analysis

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.04.033openalex-snapshot

Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.06.006openalex-snapshot

Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.12.021openalex-snapshot

Contrasting patterns of diversification between Amazonian and Atlantic forest clades of Neotropical lianas (Amphilophium, Bignonieae) inferred from plastid genomic data

inferred← citeshttps://doi.org/10.1021/acs.biochem.8b00749openalex-snapshot

Characterization of G-Quadruplexes in Chlamydomonas reinhardtii and the Effects of Polyamine and Magnesium Cations on Structure and Stability

inferred← citeshttps://doi.org/10.1038/s41467-022-29282-9openalex-snapshot

Phylotranscriptomic insights into a Mesoproterozoic–Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae)

inferred← citeshttps://doi.org/10.1038/s41598-017-01144-1openalex-snapshot

Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae

inferred← citeshttps://doi.org/10.1038/s41598-017-10409-8openalex-snapshot

Complete Chloroplast Genome Sequence of Decaisnea insignis: Genome Organization, Genomic Resources and Comparative Analysis

inferred← citeshttps://doi.org/10.1038/s41598-017-18805-wopenalex-snapshot

Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids

inferred← citeshttps://doi.org/10.1038/s41598-018-27453-7openalex-snapshot

Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae

inferred← citeshttps://doi.org/10.1038/s41598-019-44700-7openalex-snapshot

Dynamic evolution of mitochondrial genomes in Trebouxiophyceae, including the first completely assembled mtDNA from a lichen-symbiont microalga (Trebouxia sp. TR9)

inferred← citeshttps://doi.org/10.1038/srep25367openalex-snapshot

Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

inferred← citeshttps://doi.org/10.1093/dnares/dsz002openalex-snapshot

A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants

inferred← citeshttps://doi.org/10.1093/gbe/evab101openalex-snapshot

Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae

inferred← citeshttps://doi.org/10.1093/gbe/evw190openalex-snapshot

Mitochondrion-to-Chloroplast DNA Transfers and Intragenomic Proliferation of Chloroplast Group II Introns inGloeotilopsisGreen Algae (Ulotrichales, Ulvophyceae)

inferred← citeshttps://doi.org/10.1093/gbe/evy063openalex-snapshot

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

inferred← citeshttps://doi.org/10.1093/molbev/msz016openalex-snapshot

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes

inferred← citeshttps://doi.org/10.1105/tpc.19.00770openalex-snapshot

The OPR Protein MTHI1 Controls the Expression of Two Different Subunits of ATP Synthase CFo in Chlamydomonas reinhardtii

inferred← citeshttps://doi.org/10.1111/1755-0998.70143openalex-snapshot

ChloroScan : Recovering Plastid Genome Bins From Metagenomic Data

inferred← citeshttps://doi.org/10.1111/jeu.12858openalex-snapshot

Reassessment of suitable markers for taxonomy of Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes

inferred← citeshttps://doi.org/10.1111/jipb.13224openalex-snapshot

Origin and evolution of green plants in the light of key evolutionary events

inferred← citeshttps://doi.org/10.1111/jpy.12540openalex-snapshot

Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data

inferred← citeshttps://doi.org/10.1111/jpy.12928openalex-snapshot

The chloroplast genome of the lichen‐symbiont microalga Trebouxia sp. Tr9 (Trebouxiophyceae, Chlorophyta) shows short inverted repeats with a single gene and loss of the rps4 gene, which is encoded by the nucleus

inferred← citeshttps://doi.org/10.1111/jpy.70046openalex-snapshot

Extensive diversity of Symbiochlorum‐related algae from environmental sequences and culture strains supports the description of the new family Symbiochloraceae (Ulvophyceae, Chlorophyta)

inferred← citeshttps://doi.org/10.1111/jse.12248openalex-snapshot

Evolution of the Chlorophyta: Insights from chloroplast phylogenomic analyses

inferred← citeshttps://doi.org/10.1111/jse.12579openalex-snapshot

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)

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Phylogenomic subsampling: a brief review

inferred← citeshttps://doi.org/10.1127/pip/2017/0075openalex-snapshot

Molecular evolution and morphological diversification of ulvophytes (Chlorophyta)

inferred← citeshttps://doi.org/10.1186/s12862-016-0772-3openalex-snapshot

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Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes

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The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

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The signs of adaptive mutations identified in the chloroplast genome of the algae endosymbiont of Baikal sponge.

inferred← citeshttps://doi.org/10.1371/journal.pone.0184196openalex-snapshot

Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis

inferred← citeshttps://doi.org/10.1371/journal.pone.0216608openalex-snapshot

Evolution of organellar genes of chlorophyte algae: Relevance to phylogenetic inference

inferred← citeshttps://doi.org/10.1371/journal.pone.0250968openalex-snapshot

Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea

inferred← citeshttps://doi.org/10.2216/17-134.1openalex-snapshot

The hidden diversity of lichenised Trebouxiophyceae (Chlorophyta)

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Chloroplast Genome Traits Correlate With Organismal Complexity and Ecological Traits in Chlorophyta

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Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes

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Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution

inferred← citeshttps://doi.org/10.3389/fpls.2025.1534646openalex-snapshot

Comparative genomics and evolutionary analyses of Sphaeropleales

inferred← citeshttps://doi.org/10.3390/genes13101840openalex-snapshot

The Chloroplast Genome of the Lichen Photobiont Trebouxiophyceae sp. DW1 and Its Phylogenetic Implications

inferred← citeshttps://doi.org/10.3390/genes13111936openalex-snapshot

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inferred← citeshttps://doi.org/10.3390/life12030458openalex-snapshot

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inferred← citeshttps://doi.org/10.3390/md24060198openalex-snapshot

Green Extraction of Bioactive Compounds from Marine Macroalgae: Chemistry, Pharmacological Activities, and Biotechnological Applications

inferred← citeshttps://doi.org/10.3390/plants8100410openalex-snapshot

Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis

inferred← citeshttps://doi.org/10.3390/plants9080928openalex-snapshot

Complete Chloroplast Genome Characterization of Oxalis Corniculata and Its Comparison with Related Species from Family Oxalidaceae

inferred← citeshttps://doi.org/10.3390/w16131890openalex-snapshot

Influencing Factors for the Growth of Cladophora and Its Cell Damage and Destruction Mechanism: Implication for Prevention and Treatment

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Additional file 1 of The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

inferred← citeshttps://doi.org/10.6084/m9.figshare.14175649openalex-snapshot

Additional file 2 of The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

inferred← citeshttps://doi.org/10.6084/m9.figshare.14175652openalex-snapshot

Additional file 3 of The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

inferred← citeshttps://doi.org/10.6084/m9.figshare.14175655openalex-snapshot

Additional file 4 of The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

inferred← citeshttps://doi.org/10.6084/m9.figshare.14175658openalex-snapshot

Additional file 5 of The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

inferred← citeshttps://doi.org/10.6084/m9.figshare.14175661openalex-snapshot

Additional file 6 of The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

inferred← citeshttps://doi.org/10.70675/e80da54ez4400z4af2z90ccza6b6fb5b6bc7openalex-snapshot

Origins and early evolution of photosynthetic eukaryotes

inferred← citeshttps://doi.org/10.7287/peerj.2627v0.1/reviews/1openalex-snapshot

Peer Review #1 of "Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae) (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.2627v0.1/reviews/2openalex-snapshot

Peer Review #2 of "Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae) (v0.1)"

inferred← citeshttps://doi.org/10.7717/peerj.2627openalex-snapshot

Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)

inferred← citeshttps://doi.org/10.7717/peerj.6032openalex-snapshot

Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.