ArticleGenome biology and evolution2015
Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Chloroplast and mitochondrial genomes of Sphaerosorus coelastroides Pascher (Xanthophyceae) from Central Appalachia, Clinch River, Virginia, United States.Journal of phycology · 2026Article
- Lineage-Specific Retention of the Plastid tilS-trnI(CAU) Module and Its Variable Relationship With Codon Usage Evolution in Green Algae.Genome biology and evolution · 2026Article
- Chloroplast and Mitochondrial Genomes of the Lichen-Symbiotic Green Alga Trebouxia Illuminate Evolutionary Relationships and Climate Associations and Yield New Phylogenetic Markers.Genome biology and evolution · 2026Article
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Plastid genome variation in the green algal genusFrontiers in plant science · 2026Article
- Phylogenetic relationships among seven freshwater red algal genera in the Batrachospermaceae (Batrachospermales, Rhodophyta) using complete chloroplast genome data.Journal of phycology · 2025Article
- Plastomes provide new insights into phylogeny and evolution in Chlorellaceae (Chlorophyta, Trebouxiophyceae).BMC plant biology · 2025Article
- Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles.PLoS genetics · 2025Article
- Phylogenomics Untangles the Metabolic Potential of Picochlorum tauri, a New Picoalgal Species Causing a Winter Bloom in the Mediterranean Thau Lagoon.Environmental microbiology · 2025Article
- Six Newly Sequenced Chloroplast Genomes From Quadriflagellate Chlamydomonadales (Chlorophyceae): Phylogeny and Comparative Genome Analyses.Genome biology and evolution · 2025Article
- Comparative Analysis of Chloroplast Genomes inGenes · 2024Article
- Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes.Molecular biology and evolution · 2022Article
- The Chloroplast Genome of the Lichen PhotobiontGenes · 2022Article
- Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes.Frontiers in plant science · 2022Article
- Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein-coding genes.Ecology and evolution · 2022Article
- Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae.Genome biology and evolution · 2021Article
- Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data.BMC genomics · 2021Article
- Plastid Genomes of the Early Vascular Plant GenusInternational journal of molecular sciences · 2021Article
- Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution.Frontiers in plant science · 2021Article
- Variation in Plastome Sizes Accompanied by Evolutionary History in Monogenomic Triticeae (Poaceae: Triticeae).Frontiers in plant science · 2021Article
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3 authors.
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Abstract
Previous studies of trebouxiophycean chloroplast genomes revealed little information regarding the evolutionary dynamics of this genome because taxon sampling was too sparse and the relationships between the sampled taxa were unknown. We recently sequenced the chloroplast genomes of 27 trebouxiophycean and 2 pedinophycean green algae to resolve the relationships among the main lineages recognized for the Trebouxiophyceae. These taxa and the previously sampled members of the Pedinophyceae and Trebouxiophyceae are included in the comparative chloroplast genome analysis we report here. The 38 genomes examined display considerable variability at all levels, except gene content. Our results highlight the high propensity of the rDNA-containing large inverted repeat (IR) to vary in size, gene content and gene order as well as the repeated losses it experienced during trebouxiophycean evolution. Of the seven predicted IR losses, one event demarcates a superclade of 11 taxa representing 5 late-diverging lineages. IR expansions/contractions account not only for changes in gene content in this region but also for changes in gene order and gene duplications. Inversions also led to gene rearrangements within the IR, including the reversal or disruption of the rDNA operon in some lineages. Most of the 20 IR-less genomes are more rearranged compared with their IR-containing homologs and tend to show an accelerated rate of sequence evolution. In the IR-less superclade, several ancestral operons were disrupted, a few genes were fragmented, and a subgroup of taxa features a G+C-biased nucleotide composition. Our analyses also unveiled putative cases of gene acquisitions through horizontal transfer.
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