Abstract
BackgroundSimple sequence repeats (SSR), also called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects. At present, the genomes of more than 100 insect species are available. However, the features of SSRs in most insect genomes remain largely unknown.ResultsWe identified 15.01 million SSRs across 136 insect genomes. The number of identified SSRs was positively associated with genome size in insects, but the frequency and density per megabase of genomes were not. Most insect SSRs (56.2−93.1%) were perfect (no mismatch). Imperfect (at least one mismatch) SSRs (average length 22−73 bp) were longer than perfect SSRs (16−30 bp). The most abundant insect SSRs were the di- and trinucleotide types, which accounted for 27.2% and 22.0% of all SSRs, respectively. On average, 59.1%, 36.8%, and 3.7% of insect SSRs were located in intergenic, intronic, and exonic regions, respectively. The percentages of various types of SSRs were similar among insects from the same family. However, they were dissimilar among insects from different families within orders. We carried out a phylogenetic analysis using the SSR frequencies. Species from the same family were generally clustered together in the evolutionary tree. However, insects from the same order but not in the same family did not cluster together. These results indicated that although SSRs undergo rapid expansions and contractions in different populations of the same species, the general genomic features of insect SSRs remain conserved at the family level.ConclusionMillions of insect SSRs were identified and their genome features were analyzed. Most insect SSRs were perfect and were located in intergenic regions. We presented evidence that the variance of insect SSRs accumulated after the differentiation of insect families.
Highlights
Simple sequence repeats (SSR), called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects
The number, density and relative abundance of SSRs in 136 insect genomes We identified a total of 15.01 million SSRs from 136 insect genomes (Additional file 1: Table S1)
The number of SSRs is positively correlated with genome size (Spearman’s rho = 0.499, P < 0.001), indicating that the abundance of SSRs varies greatly with insect species (Fig. 1)
Summary
Simple sequence repeats (SSR), called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects. Simple sequence repeats (SSR), known as microsatellites, are tandem repetitions of 1–6 bp motifs that are found in all eukaryotic genomes [1]. SSR diversity has been extensively surveyed in more than 200 insects to validate their use as molecular markers to infer the demography and relationships of closely related populations or species [10, 18, 19]. A comparative analysis of SSRs occurring within protein-coding regions of 25 insect species suggested that these repeats represent characteristic features of insect genome diversity [13]. We investigated SSRs in 136 insect species, representing 16 taxonomic orders. Cluster and divergence analysis based on the frequencies of various SSRs were performed
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