Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes

Abstract

Microsatellites or simple sequence repeats (SSRs) have been found in most organisms during the last decade. Since large-scale sequences are being generated, especially those that can be used to search for microsatellites, the development of these markers is getting more convenient. Keeping SSRs in viewing the importance of the application, available CDS (coding sequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study the frequency and density of various types of microsatellites. On the basis of surveying CDS or EST sequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse, 34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb in silkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mouse, 1/1.25 Kb in zebrafish and 1/1.38 Kb in C. elegans. The overall average SSR frequency of these species is 1/1.07 Kb. Hexanucleotide repeats (64.5%-76.6%) are the most abundant class of SSR in the investigated species, followed by trimeric, dimeric, tetrameric, monomeric and pentameric repeats. Furthermore, the A-rich repeats are predominant in each type of SSRs, whereas G-rich repeats are rare in the coding regions.

Fig. 1

Comparison of densities of each SSR across the eukaryotic genomes. The density is expressed in base-pairs of SSRs sequence per megabase-pairs of dataset sequences.

Fig. 2

Comparative analysis of redundant and non-redundant SSRs in silkworm EST set. Redundant SSRs were identified in total set of ESTs (116,914), and non-redundant SSRs were identified in non-redundant set of ESTs (14,081) and were selected after assembling.

Fig. 3

Distribution of SSRs in eukaryotic genomes. In all species hexameric repeats are the most frequent followed by trimeric repeats, while penatameric repeats are under 2% of the total number of SSRs.

Fig. 4

An example of the distribution of microsatellites of different repeat units in ESTs of silkworm. The number of SSRs in a particular class decreases with the increasing number of repeat units.

Fig. 5

Density of different dimeric repeats per million base pairs of CDS or ESTs sequences in different genomes.

Fig. 6

Density of different trimeric repeats per million base pairs of CDS or ESTs sequences in different genomes.

Fig. 7

Density of different tetrameric repeats per million base pairs of CDS or ESTs sequences in different genomes.