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

@article{Brouard2016ProliferationOG,
  title={Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)},
  author={Jean-Simon Brouard and Monique Turmel and Christian Otis and Claude Lemieux},
  journal={PeerJ},
  year={2016},
  volume={4}
}
Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and… Expand
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References

SHOWING 1-10 OF 83 REFERENCES
Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum
TLDR
The comparative genome analyses in a phylogenetic framework inferred an evolutionary scenario of the mutational events that led to changes in genome architecture in the Chlorophyceae, and suggested that the Stigeoclonium genome replicates bidirectionally from a single origin. Expand
The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae
TLDR
Parsimony analysis of structural genomic features and phylogenetic analysis of chloroplast sequence data unambiguously resolved the Oedogoniales as sister to the Chaetopeltidales and Chaetophorales. Expand
The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands
TLDR
Owing to this plasticity, only a sketchy portrait could be drawn for the chloroplast genome of the last common ancestor of Scenedesmus and Chlamydomonas, the results underscore the remarkable plasticity of the chlorophycean chloropleft genome. Expand
Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer
TLDR
The complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales) is described, which provides a clear example that novel genes were acquired by the chloroplast genome through horizontal transfers, possibly from a mitochondrial genome donor. Expand
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.
TLDR
It is revealed that major reduction in gene content and restructuring of the chloroplast genome occurred in conjunction with important changes in cell organization in at least two independent prasinophyte lineages, the Mamiellales and the Pycnococcaceae. Expand
The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes
TLDR
The complete cpDNA sequence of Oltmannsiellopsis viridis is determined, a representative of a distinct, early diverging lineage of the Ulvophyceae, and comparative analyses of chlorophyte cpDNAs support the notion that the ulvophyte homologue is sister to the Chlorophycesae. Expand
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.
TLDR
Phylogenetic analyses of 58 cpDNA-encoded proteins and genes support the hypothesis that the Ulvophyceae is sister to the Trebouxiophyeae but cannot eliminate the hypothesis That the ULVophycee is sisters to the Chlorophycees. Expand
Distinctive Architecture of the Chloroplast Genome in the Chlorodendrophycean Green Algae Scherffelia dubia and Tetraselmis sp. CCMP 881
TLDR
Some of the phylogenomic trees inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Expand
The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes.
  • M. Turmel, C. Otis, C. Lemieux
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1999
TLDR
The complete chloroplast DNA sequence of Nephroselmis olivacea, a member of the class (Prasinophyceae) thought to include descendants of the earliest-diverging green algae, is determined and phylogenetic analyses offer insight into the chlorophyte ancestor of euglenophyte chloroplasts. Expand
The Chloroplast Genome of the Green Alga Schizomeris leibleinii (Chlorophyceae) Provides Evidence for Bidirectional DNA Replication from a Single Origin in the Chaetophorales
TLDR
The results support the notion that these two chaetophoralean genomes replicate bidirectionally from a putative origin located in the vicinity of the small subunit ribosomal RNA gene. Expand
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