help button home button Genetics AJP: Renal Phys
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Ardell, D. H.
Right arrow Articles by Landweber, L. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ardell, D. H.
Right arrow Articles by Landweber, L. F.
Genetics, Vol. 165, 1761-1777, December 2003, Copyright © 2003

Polymorphism, Recombination and Alternative Unscrambling in the DNA Polymerase {alpha} Gene of the Ciliate Stylonychia lemnae (Alveolata; class Spirotrichea)

David H. Ardella,b, Catherine A. Lozuponeb, and Laura F. Landweberb
a Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, SE-752 36 Uppsala, Sweden
b Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544

Corresponding author: David H. Ardell, Box 596, Biomedical Center, Uppsala University, SE-751 24 Uppsala, Sweden., dave.ardell{at}icm.uu.se (E-mail)

Communicating editor: M. FELDMAN

DNA polymerase {alpha} is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D.




This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
S. Kuo, W.-J. Chang, and L. F. Landweber
Complex Germline Architecture: Two Genes Intertwined on Two Loci
Mol. Biol. Evol., January 1, 2006; 23(1): 4 - 6.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
W.-J. Chang, P. D. Bryson, H. Liang, M. K. Shin, and L. F. Landweber
The evolutionary origin of a complex scrambled gene
PNAS, October 18, 2005; 102(42): 15149 - 15154.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2003 by the Genetics Society of America.