Selection on the structural stability of a ribosomal RNA expansion segment in Daphnia obtusa

McTaggart S.J. and Crease T.J. (2005) Selection on the structural stability of a ribosomal RNA expansion segment in Daphnia obtusa. Molecular Biology and Evolution, 22 5: 1309-1319. doi:10.1093/molbev/msi119


Author McTaggart S.J.
Crease T.J.
Title Selection on the structural stability of a ribosomal RNA expansion segment in Daphnia obtusa
Journal name Molecular Biology and Evolution   Check publisher's open access policy
ISSN 0737-4038
Publication date 2005-01-01
Year available 2005
Sub-type Article (original research)
DOI 10.1093/molbev/msi119
Open Access Status
Volume 22
Issue 5
Start page 1309
End page 1319
Total pages 11
Publisher OXFORD UNIV PRESS
Language eng
Subject 1101 Medical Biochemistry and Metabolomics
1105 Dentistry
1300 Biochemistry, Genetics and Molecular Biology
1303 Specialist Studies in Education
1311 Genetics
1312 Molecular Biology
2716 Genetics (clinical)
Abstract The high rate of sequence divergence in nuclear ribosomal RNA (rRNA) expansion segments offers a unique opportunity to study the importance of natural selection in their evolution. To this end, we polymerase chain reaction amplified and cloned a 589-nt fragment of the 18S rRNA gene containing expansion segments 43/e1 and 43/e4 from six individual Daphnia obtusa from four populations. We screened 2,588 clones using single-stranded conformation polymorphism analysis and identified 103 unique haplotype sequences. We detected two pairs of indel sites in segment 43/e4 that complement each other when the secondary structure of the linear sequence is formed. Seven of the 12 observed combinations of length variants at these four sites (haplotypes) are shared between individuals from different populations, which may suggest that some of the length variation was present in their common ancestor. Haplotypes with uncompensated indels were only observed at low frequencies, while compensated indel haplotypes were found at a wide range of frequencies, supporting the hypothesis that the energetic stability of expansion segments is a trait under natural selection. In addition, there was strong linkage disequilibrium between the four complementary indel sites, particularly those that pair with one another in the secondary structure. Despite selection against unpaired bulges at these four indel sites, some nucleotides that form unpaired bulges are highly conserved in segment 43/e4, indicating that they are under a different selective constraint, possibly due to their role in higher level structural interactions.
Keyword Daphnia obtusa
Expansion segment
Ribosomal RNA
Secondary structure
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
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Citation counts: TR Web of Science Citation Count  Cited 12 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 12 times in Scopus Article | Citations
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