Complex Patterns of Plastid 16S rRNA Gene Evolution in Nonphotosynthetic Green Algae

@article{Nedelcu2014ComplexPO,
  title={Complex Patterns of Plastid 16S rRNA Gene Evolution in Nonphotosynthetic Green Algae},
  author={Aurora M. Nedelcu},
  journal={Journal of Molecular Evolution},
  year={2014},
  volume={53},
  pages={670-679}
}
  • A. Nedelcu
  • Published 1 December 2001
  • Biology
  • Journal of Molecular Evolution
This study provides a phylogenetic/comparative approach to deciphering the processes underlying the evolution of plastid rRNA genes in genomes under relaxed functional constraints. Nonphotosynthetic green algal taxa that belong to two distinct classes, Chlorophyceae (Polytoma) and Trebouxiophyceae (Prototheca), were investigated. Similar to the situation described previously for plastid 16S rRNA genes in nonphotosynthetic land plants, nucleotide substitution levels, extent of structural… 
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References

SHOWING 1-10 OF 54 REFERENCES
Do nonasterid holoparasitic flowering plants have plastid genomes?
TLDR
Preliminary evidence is provided of the retention of highly diverged and truncated plastid genome in Cytinus and the greater sequence divergence for 16S rDNA and the negative hybridization results for Hydnora and Corynaea suggests two possibilities: the loss of typically conserved elements of their plastomes or the complete absence of a plastome.
Characterization of Mitochondrial Small-Subunit Ribosomal RNAs from Holoparasitic Plants
TLDR
Mitochondrial small-subunit (19S) rDNA sequences were obtained from 10 angiosperms to further characterize sequence divergence levels and structural variation in this molecule and confirmed the accelerated nucleotide substitution rates in the holoparasites whereas rates in nonparasitic plants were not significantly increased.
Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant.
Complete nucleotide sequencing shows that the plastid genome of Epifagus virginiana, a nonphotosynthetic parasitic flowering plant, lacks all genes for photosynthesis and chlororespiration found in
Alternate paths of evolution for the photosynthetic gene rbcL in four nonphotosynthetic species of Orobanche
TLDR
Comparison of rbcL 3'-UTR sequences for Nicotiana, Ipomoea, Cuscuta, and Orobanche reveal that nucleotide sequences from parasitic plants have regions capable of forming stem-loop structures, but 56–69 nt are deleted upstream of the stem- loop in the parasitic plants compared to their photosynthetic relatives.
Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma.
TLDR
Two plastid genes--rrn16, encoding the plastsid small-subunit rRNA, and tufA, encoding elongation factor Tu--retain their functions in protein synthesis after the loss of photosynthesis in two nonphotosynthetic Polytoma clades but show a substantially accelerated rate of base substitution in the P. uvella clade.
Structural analyses of plastid-derived 16S rRNAs in holoparasitic angiosperms
TLDR
Higher-order structures have been constructed for plastid-encoded small-subunit (SSU, 16S), rRNAs from representatives of seven nonphotosynthetic holoparasitic angiosperm families and it is shown that relaxation of selection pressure on ribosome function resulting in altered DNA replication and/or repair systems may be involved.
The rbcL gene from the non-photosynthetic parasite Lathraea clandestina is not transcribed by a plastid-encoded RNA polymerase
TLDR
Similarity to non-consensus E. coli-like plastid promoters suggests that rbcL transcription is driven by a nuclear-encoded RNA polymerase.
A divergent plastid genome inConopholis americana, an achlorophyllous parasitic plant
TLDR
The plastid genome of Conopholis americana, a totally achlorophyllous angiosperm which exists as a root parasite on red oaks, is investigated to find that it is maintained in high copy number in fruit tissue, whereas mature seeds have an approximately 10-fold lower copy number.
Organization and sequence of photosynthetic genes from the plastid genome of the holoparasitic flowering plant Cuscuta reflexa
TLDR
An area of about 6 kb of the plastid DNA (ptDNA) from the holoparasitic plant Cuscuta refexa is cloned and sequenced, which contains the rbcL gene, which encodes a polypeptide which is 18–23 amino acids longer than in other higher plants.
Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: many losses of photosynthesis and complex patterns of rate variation.
TLDR
It is suggested that there may be substantial molecular evolutionary changes to the plastid genome of parasites before the loss of photosynthesis, and independent patterns of synonymous and nonsynonymous rate acceleration in rps2 point to distinct mechanisms underlying rate variation in different lineages.
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