MBE Advance Access published online on March 22, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm059
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Research Article |
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
* Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan
School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
E-Mial: smchaw{at}sinica.edu.tw
Received for publication December 25, 2006. Revision received March 7, 2007. Accepted for publication March 15, 2007.
Phylogenetic relationships among the five groups of extant seed plants are presently unsettled. To re-examine this long-standing debate, we determine the complete chloroplast genome (cpDNA) of Cycas taitungensis and 56 protein-coding genes encoded in the cpDNA of Gnetum parvifolium. The cpDNA of Cycas is a circular molecule of 163,403 bp with two typical large inverted repeats (IRs) of 25,074 bp each. We inferred phylogenetic relationships among major seed plant lineages using concatenated 56 protein-coding genes in 37 land plants. Phylogenies generated by use of three independent methods provide concordant and robust support for the monophylies of extant seed plants, gymnosperms, and angiosperms. Within the modern gymnosperms are two highly supported sister clades: Cycas-Ginkgo and Gnetum-Pinus. This result agrees with both the "gnetifer" and "gnepines" hypotheses. The sister relationships in Cycas-Ginkgo and Gnetum-Pinus clades are further reinforced by cpDNA structural evidence. Branch lengths of Cycas-Ginkgo and Gnetum were consistently the shortest and the longest, respectively in all separate analyses. However, the Gnetum relative rate test revealed this tendency only for the third codon positions and the transversional sites of the first two codon positions. A 
tufA located between psbE and petL genes is here first detected in Anthoceros (a hornwort), cycads and Ginkgo. We demonstrate that the tufA is a footprint descended from the chloroplast tufA of green algae. The duplication of ycf2 genes and their shift into IRs should have taken place at least in the common ancestor of seed plants more than 300 million years ago (MYA), and the tRNAPro-GGG gene was lost from the angiosperm lineage at least 150 MYA. Additionally, from cpDNA structural comparison, we propose an alternative model for the loss of large IR regions in black pine. More cpDNA data from non-Pinaceae conifers are necessary to justify whether the "gnetifer" or "gnepines" hypothesis is valid and to generate solid structural evidence for the monophyly of extant gymnosperms.
Key Words: Cycas taitungensis • Gnetum parvifolium • Ginkgo • chloroplast genome • gymnosperms • seed plants • phylogeny • evolution • substitution rate
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