Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana

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.

Computational Mining of Microsatellites in the Chloroplast Genome of Ptilidium pulcherrimum, a Liverwort

“…These repeats consist of short repeat motifs of 1-6 bp and are present in both coding and non-coding regions of DNA sequences (Shanker et al, 2007). SSRs have been widely used as molecular markers in plant genomes (Gupta et al, 2003;Jakobsson et al, 2007;Blair and Hurtado, 2013). Apart from this, a database named MitoSatPlant has been developed which provides information about mitochondrial SSRs of green plants (Kumar et al, 2014).…”

Cytoplasmic diversity of Brassica napus L., Brassica oleracea L. and Brassica rapa L. as determined by chloroplast microsatellite markers

“…Nearly all of the cpSSR markers detected are of the mononucleotide type (Flannery et al 2006;Jakobsson et al 2007). Using a limited set of cpSSR markers for studying cytoplasmic diversity in oilseed rape has led to differing results (Flannery et al 2006;Jakobsson et al 2007;Allender and King 2010). The identification of a set of most informative cpSSR primer pairs for the Brassica AA, CC and AACC genomes could be most useful in future work for the characterization and evaluation of the effects of different cytoplasms in oilseed rape.…”

“…Ebert and Peakall (2009) emphasized that cpSSR repeats are likely more abundant in intergenic spacer regions than in introns. Nearly all of the cpSSR markers detected are of the mononucleotide type (Flannery et al 2006;Jakobsson et al 2007). Using a limited set of cpSSR markers for studying cytoplasmic diversity in oilseed rape has led to differing results (Flannery et al 2006;Jakobsson et al 2007;Allender and King 2010).…”

“…Chloroplast specific SSR-markers (cpSSR) have been developed for a number of species including Arabidopsis (Weising and Gardner 1999;Provan 2000;Jakobsson et al 2007;Haider 2011) and oilseed rape (Provan 2000;Flannery et al 2006;Allender et al 2007). Chloroplast cpSSR repeats may be found in both coding and non-coding regions but more variation were reported in the non-coding regions including introns and intergenic spacer of cpDNA (Provan et al 2001;Jakobsson et al 2007). Ebert and Peakall (2009) emphasized that cpSSR repeats are likely more abundant in intergenic spacer regions than in introns.…”

Simple sequence repeats mining using computational approach in chloroplast genome of Marchantia polymorpha

“…These repeats are present in both coding and non-coding regions of DNA sequences, and have been widely used as molecular markers in plant genomes (Gupta et al, 2003;Jakobsson et al, 2007;Blair & Hurtado, 2013). Studies were conducted to mine SSRs in chloroplast genomes of bryophytes (Shanker, 2013d,e).…”