Skip Navigation


MBE Advance Access originally published online on October 5, 2005
Molecular Biology and Evolution 2006 23(2):279-291; doi:10.1093/molbev/msj029
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow Supplementary Material
Right arrow All Versions of this Article:
23/2/279    most recent
msj029v2
msj029v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (23)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Chang, C.-C.
Right arrow Articles by Chaw, S.-M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chang, C.-C.
Right arrow Articles by Chaw, S.-M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae): Comparative Analysis of Evolutionary Rate with that of Grasses and Its Phylogenetic Implications

Ching-Chun Chang*,1, Hsien-Chia Lin*,1, I-Pin Lin{dagger}, Teh-Yuan Chow{ddagger},2, Hong-Hwa Chen*, Wen-Huei Chen§, Chia-Hsiung Cheng{ddagger}, Chung-Yen Lin||, Shu-Mei Liu{ddagger}, Chien-Chang Chang and Shu-Miaw Chaw

* Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan; {dagger} Department of Superintendent, Tainan Municipal Hospital, Tainan, Taiwan; {ddagger} Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan; § Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan; || Institute of Information Science, Academia Sinica, Taipei, Taiwan; and Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan

E-mail: smchaw{at}sinica.edu.tw.

Whether the Amborella/Amborella-Nymphaeales or the grass lineage diverged first within the angiosperms has recently been debated. Central to this issue has been focused on the artifacts that might result from sampling only grasses within the monocots. We therefore sequenced the entire chloroplast genome (cpDNA) of Phalaenopsis aphrodite, Taiwan moth orchid. The cpDNA is a circular molecule of 148,964 bp with a comparatively short single-copy region (11,543 bp) due to the unusual loss and truncation/scattered deletion of certain ndh subunits. An open reading frame, orf91, located in the complementary strand of the rrn23 was reported for the first time. A comparison of nucleotide substitutions between P. aphrodite and the grasses indicates that only the plastid expression genes have a strong positive correlation between nonsynonymous (Ka) and synonymous (Ks) substitutions per site, providing evidence for a generation time effect, mainly across these genes. Among the intron-containing protein-coding genes of the sampled monocots, the Ks of the genes are significantly correlated to transitional substitutions of their introns. We compiled a concatenated 61 protein-coding gene alignment for the available 20 cpDNAs of vascular plants and analyzed the data set using Bayesian inference, maximum parsimony, and neighbor-joining (NJ) methods. The analyses yielded robust support for the Amborella/Amborella-Nymphaeales-basal hypothesis and for the orchid and grasses together being a monophyletic group nested within the remaining angiosperms. However, the NJ analysis using Ka, the first two codon positions, or amino acid sequences, respectively, supports the monocots-basal hypothesis. We 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.

Key Words: Phalaenopsis aphrodite • chloroplast genome • angiosperms • phylogeny • Orchidaceae • Poaceae • substitution rate • molecular evolution


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
R. Lahaye, M. van der Bank, D. Bogarin, J. Warner, F. Pupulin, G. Gigot, O. Maurin, S. Duthoit, T. G. Barraclough, and V. Savolainen
From the Cover: DNA barcoding the floras of biodiversity hotspots
PNAS, February 26, 2008; 105(8): 2923 - 2928.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. J. Wickett, Y. Zhang, S. K. Hansen, J. M. Roper, J. V. Kuehl, S. A. Plock, P. G. Wolf, C. W. dePamphilis, J. L. Boore, and B. Goffinet
Functional Gene Losses Occur with Minimal Size Reduction in the Plastid Genome of the Parasitic Liverwort Aneura mirabilis
Mol. Biol. Evol., February 1, 2008; 25(2): 393 - 401.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. K. Jansen, Z. Cai, L. A. Raubeson, H. Daniell, C. W. dePamphilis, J. Leebens-Mack, K. F. Muller, M. Guisinger-Bellian, R. C. Haberle, A. K. Hansen, et al.
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
PNAS, December 4, 2007; 104(49): 19369 - 19374.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C.-S. Wu, Y.-N. Wang, S.-M. Liu, and S.-M. Chaw
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
Mol. Biol. Evol., June 1, 2007; 24(6): 1366 - 1379.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
W.-H. Zeng, S.-C. Liao, and C.-C. Chang
Identification of RNA Editing Sites in Chloroplast Transcripts of Phalaenopsis aphrodite and Comparative Analysis with Those of Other Seed Plants
Plant Cell Physiol., February 1, 2007; 48(2): 362 - 368.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
R. M. Bateman, J. Hilton, and P. J. Rudall
Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers
J. Exp. Bot., October 1, 2006; 57(13): 3471 - 3503.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.