Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.

@article{Chaw2000SeedPP,
  title={Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.},
  author={Shu-Miaw Chaw and Christopher L. Parkinson and Y. J. Cheng and Teresa Vincent and Jeffrey D. Palmer},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2000},
  volume={97 8},
  pages={
          4086-91
        }
}
  • S. Chaw, C. Parkinson, J. Palmer
  • Published 11 April 2000
  • Biology
  • Proceedings of the National Academy of Sciences of the United States of America
Phylogenetic relationships among the five groups of extant seed plants are presently quite unclear. For example, morphological studies consistently identify the Gnetales as the extant sister group to angiosperms (the so-called "anthophyte" hypothesis), whereas a number of molecular studies recover gymnosperm monophyly, and few agree with the morphology-based placement of Gnetales. To better resolve these and other unsettled issues, we have generated a new molecular data set of mitochondrial… 

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Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants.
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The complete chloroplast genome of Cycas taitungensis and 56 protein-coding genes encoded in the cpDNA of Gnetum parvifolium are determined and it is demonstrated that the PsitufA is a footprint descended from the chloropstroke tufA of green algae.
Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes
TLDR
This study uses LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera and strongly supports cycads as the basal-most lineage of Gymnosperms rather than sister to Ginkgoaceae.
Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes
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Comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloropleft genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.
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