Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: Revised molecular estimates of two seed plant divergence times

@article{Goremykin2004EvolutionaryAO,
  title={Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: Revised molecular estimates of two seed plant divergence times},
  author={Vadim V. Goremykin and Sabine Hansmann and William F. Martin},
  journal={Plant Systematics and Evolution},
  year={2004},
  volume={206},
  pages={337-351}
}
Fifty-eight homologous protein sequences from the completely sequenced chloroplast genomes ofZea mays, Oryza sativa, Nicotiana tabacum, Pinus thunbergii, Marchantia polymorpha andPoryphyra purpurea were investigated. Analyzed individually, only 40 of the 58 proteins gave the true, known topology for these species. Trees constructed from the concatenated 14295 amino acid alignment and from automatically generated subsets of the data containing successively fewer polymorphisms were used to… 
Molecular data from 27 proteins do not support a Precambrian origin of land plants.
  • M. Sanderson
  • Environmental Science
    American journal of botany
  • 2003
TLDR
This paper presents an analysis of an entirely different set of sequence data from 27 plastid protein-coding genes in 10 land plants and a green algal outgroup that leads to estimates ranging from 425 to 490 mya, which brackets the age suggested by the fossil record.
Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor.
TLDR
The genome-wide frequency of gene acquisitions from cyanobacteria in 4 photosynthetic eukaryotes is reported, consistent with suggestions that fixed nitrogen supplied by the endosymbiont might have played an important role during the origin of plastids.
Dating the Monocot–Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes
TLDR
It is proposed that monocots branched off from dicots 140–150 Myr ago, at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100–115 Myr ago (Albian–Aptian of the Cretaceous).
The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications.
TLDR
It is demonstrated that these conflicting angiosperm phylogenies are most probably linked to the transitional sites at all codon positions, especially at the third one where the strong base-composition bias and saturation effect take place.
Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of Amborella and Ceratophyllum
TLDR
It is shown that support of the basal-most position of Amborella trichopoda among the angiosperms in the chloroplast genomic data is based only on a tiny subset of the most variable positions in alignment, exhibiting mean maximum likelihood (ML) distance among theAngiosperm operational taxonomic units (OTUs) approximately 36 substitutions/site.
The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm.
TLDR
Phylogenetic analyses of the chloroplast DNA of Nymphaea alba revealed consistent support for Nympholia being a divergent member of a monophyletic dicot assemblage and observations suggesting that the monocot lineage leading to the grasses has the strongest phylogenetic affinity to gymnosperms have general implications for studies of substitution model specification and analyses of concatenated genome data.
Phylogeny of flowering plants by the chloroplast genome sequences: in search of a “lucky gene”
TLDR
The RNA polymerase genes are compactly arranged in the genome and are fourfold shorter than the total length of protein coding genes used for phylogenetic analysis, which makes this group of genes main candidates for the role of “lucky gene” in studying phylogeny of flowering plants.
An update on chloroplast genomes
TLDR
This review aims to summarize the progress in chloroplast genome research since its inception and tries to encompass all related aspects, including RNA editing, ycfs, molecular phylogeny, DNA barcoding as well as gene transfer to the nucleus.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 53 REFERENCES
Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data.
TLDR
The results imply that the angiosperm lineage emerged in Jurassic-Triassic time, which considerably predates its appearance in the fossil record (approximately 120 Myr ago), which can be taken as an upper bound for the age of angiosperms.
Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants.
TLDR
Phylogenetic analyses of nucleotide sequences indicated that the earliest divergence of extant seed plants is likely represented by a split between conifer-cycad and angiosperm lineages, which implies a substantially more recent ancestor of all extant plant plants than suggested by some theories of plant evolution.
Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii.
TLDR
All 11 functional genes (ndh genes) for subunits of a putative NADH dehydrogenase that are found in the chloroplast genomes of angiosperms and a bryophyte are lost, raising the possibility that all ndh genes have been transferred to the nucleus or that an NADH dehydration is not essential in black pine chloroplasts.
The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals
TLDR
The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.
The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression
TLDR
Five sequences coding for proteins homologous to components of the respiratory‐chain NADH dehydrogenase from human mitochondria have been found and sequence and expression analyses indicate both prokaryotic and eukaryotic features of the chloroplast genes.
Estimation of the monocot–dicot age through tRNA sequences from the chloroplast
TLDR
Using chloroplast tRNA sequences and evidence of absolute time estimates of splits within plant evolution, the monocot–dicot divergence is calculated to be somewhere between 230 to 350 Ma before present (BP).
Extensive variation in evolutionary rate of rbcL gene sequences among seed plants.
TLDR
Within angiosperms, the annual forms evolved more rapidly, on average, than perennial forms, and this rate heterogeneity was more extensive at nonsynonymous sites than synonymous ones, and it resulted primarily from a recent acceleration of substitution rate in many groups of angios perms.
Molecular phylogenies in angiosperm evolution.
TLDR
Cloned and sequenced cDNAs for the glyceraldehyde-3-phosphate dehydrogenase of glycolysis, gapC, from a bryophyte, a gymnosperm, and three angiosperms and chloroplast and nuclear sequence data taken together suggest that the separation of monocotyledonous and dicotylingonous lineages took place in late Carboniferous times.
Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing.
TLDR
A survey of the 25 editing positions identified in 13 different transcripts of the maize plastome shows that representatives of all protein coding gene classes are subject to editing, particularly for the second codon position and for certain codon transitions.
The time of origin of the flowering plants determined by using amino acid sequence data of cytochrome c
Summary Cytochrome c sequences from nineteen plants have been used, in conjunction with those of animal and fungal origin already published, to calculate the times of origin of the animal, fungal
...
1
2
3
4
5
...