MBE Advance Access published online on December 24, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm241
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Research Article |
Reevaluation of the cox1 Group I Intron in Araceae and Angiosperms Indicates a History Dominated by Loss rather than Horizontal Transfer
1 Department of Biology, Ludwig Maximilian University, D-80638 Munich, Germany
2 The Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166-0299, USA, and Chengdu Institute of Biology, Chinese Academy of Sciences, P. O. Box 416, Chengdu, Sichuan 610041, P. R. China
* Corresponding author. Present address: Menzinger Str. 67, 80638 Munich, Phone: +49 89 17861 251, Fax: +49 89 172638, E-mail address: cusimano{at}lrz.uni-muenchen.de
Received for publication September 4, 2007. Revision received October 12, 2007. Accepted for publication October 30, 2007.
The origin and modes of transmission of introns remain matters of much debate. Previous studies of the group I intron in the angiosperm cox1 gene inferred frequent angiosperm-to-angiosperm horizontal transmission of the intron from apparent incongruence between intron phylogenies and angiosperm phylogenies, patchy distribution of the intron among angiosperms, and differences between cox1 exonic coconversion tracts (the first 22 nucleotides downstream of where the intron inserted). We analyzed the cox1 gene in 179 angiosperms, 110 of them containing the intron (intron+) and 69 lacking it (intron-). Our taxon sampling in Araceae is especially dense to test hypotheses about vertical and horizontal intron transmission put forward by Cho and Palmer (1999). Maximum likelihood trees of Araceae cox1 introns, and also of all-angiosperm cox1 introns, are largely congruent with known phylogenetic relationships in these taxa. The exceptions can be explained by low signal in the intron and long-branch attraction among a few taxa with high mitochondrial substitution rates. Analysis of the 179 coconversion tracts reveals 20 types of tracts (11 of them only found in single species, all involving silent substitutions). The distribution of these tracts on the angiosperm phylogeny shows a common ancestral type, characterizing most intron+ and some intron– angiosperms, and several derivative tract types arising from gradual back mutation of the coconverted nucleotides. Molecular clock dating of small intron+ and intron– sister clades suggests that coconversion tracts have persisted for 70 million years in Araceae, whose cox1 sequences evolve comparatively slowly. Sequence similarity among the 110 introns ranges from 91% to identical, while putative homologs from fungi are highly different, but sampling in fungi is still sparse. Together, these results suggest that the cox1 intron entered angiosperms once, has since largely or entirely been transmitted vertically, and has been lost numerous times, with coconversion tract footprints providing unreliable signal of former intron presence.
Key Words: group I intron • mitochondrial genome • cox1 gene • horizontal gene transfer • coconversion • angiosperms
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  M. V. Sanchez-Puerta, Y. Cho, J. P. Mower, A. J. Alverson, and J. D. Palmer Frequent, Phylogenetically Local Horizontal Transfer of the cox1 Group I Intron in Flowering Plant Mitochondria Mol. Biol. Evol., August 1, 2008; 25(8): 1762 - 1777. [Abstract] [Full Text] [PDF]
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