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Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana

Jakobsson, Mattias LU ; Säll, Torbjörn LU ; Lind-Hallden, Christina and Halldén, Christer LU (2007) In Theoretical And Applied Genetics 114(2). p.223-235
Abstract
The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the... (More)
The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated-such as the position of a locus within the chromosome, or imperfect repeats-appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Theoretical And Applied Genetics
volume
114
issue
2
pages
223 - 235
publisher
Springer
external identifiers
  • wos:000242855700003
  • scopus:33845912434
ISSN
0040-5752
DOI
10.1007/s00122-006-0425-9
language
English
LU publication?
yes
id
758628cb-7712-44aa-8fd8-8bd78327fbaa (old id 680478)
date added to LUP
2007-12-13 10:09:22
date last changed
2017-10-01 04:36:13
@article{758628cb-7712-44aa-8fd8-8bd78327fbaa,
  abstract     = {The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated-such as the position of a locus within the chromosome, or imperfect repeats-appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.},
  author       = {Jakobsson, Mattias and Säll, Torbjörn and Lind-Hallden, Christina and Halldén, Christer},
  issn         = {0040-5752},
  language     = {eng},
  number       = {2},
  pages        = {223--235},
  publisher    = {Springer},
  series       = {Theoretical And Applied Genetics},
  title        = {Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1007/s00122-006-0425-9},
  volume       = {114},
  year         = {2007},
}