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Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.
- S. Chaw, C. Parkinson, Y. Cheng, T. Vincent, J. Palmer
- BiologyProceedings of the National Academy of Sciences…
- 11 April 2000
The Gnetales may be viewed as extremely divergent conifers, and the many morphological similarities between angiosperms and G netales arose independently.
Dating the Monocot–Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes
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.
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.
Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences.
To study the evolutionary relationships among the four living gymnosperm orders and the interfamilial relationships in each order, a set of 65 nuclear 18S rRNA sequences from ferns, gymnosperms, and…
The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites.
- S. Chaw, A. C. Shih, Daryi Wang, Yu-Wei Wu, Shu-Mei Liu, The-Yuan Chou
- BiologyMolecular biology and evolution
- 1 March 2008
The mtDNA of Cycas taitungensis is a circular molecule of 414,903 bp, making it 2- to 6-fold larger than the known mtDNAs of charophytes and bryophytes, but similar to the average of 7 elucidated…
Comparative Chloroplast Genomics Reveals the Evolution of Pinaceae Genera and Subfamilies
- Ching-Ping Lin, Jen-Pan Huang, Chung-Shien Wu, Chih-Yao Hsu, S. Chaw
- BiologyGenome biology and evolution
- 2 July 2010
The phylogenetic analyses reveal that Cedrus is clustered with Abies–Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix–Pseudotsuga, and views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.
Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots
- Rui‐Jiang Wang, Chiao-Lei Cheng, Ching-Chun Chang, Chun-Lin Wu, T. Su, S. Chaw
- BiologyBMC Evolutionary Biology
- 31 January 2008
The RT-PCR assays indicate that in monocot IRA the trnH-rps19 gene cluster is regulated by two opposing promoters, S10Aand psbA, which implies that the duplication of trnh- rps19 genes in the IRB of most monocots and non-monocot angiosperms have distinct fates, which are likely regulated by different expression levels of S 10Aand S10B promoters.
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.
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.
Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny
- Chung-Shien Wu, Ya-nan Wang, Chih-Yao Hsu, Ching-Ping Lin, S. Chaw
- BiologyGenome biology and evolution
- 19 September 2011
Based on a structural finding, the character of an IR loss no longer conflicts with the “gnepines” hypothesis (gnetophytes sister to Pinaceae), and chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, it was demonstrated that high heterotachous genes contributed to the long-branch attraction (LBA) artifact, resulting inincongruence of phylogenomic estimates.