Differential Distribution of Simple Sequence Repeats in Eukaryotic Genome Sequences

Abstract

Complete chromosome/genome sequences available from humans, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Saccharomyces cerevisiae were analyzed for the occurrence of mono-, di-, tri-, and tetranucleotide repeats. In all of the genomes studied, dinucleotide repeat stretches tended to be longer than other repeats. Additionally, tetranucleotide repeats in humans and trinucleotide repeats in Drosophila also seemed to be longer. Although the trends for different repeats are similar between different chromosomes within a genome, the density of repeats may vary between different chromosomes of the same species. The abundance or rarity of various di- and trinucleotide repeats in different genomes cannot be explained by nucleotide composition of a sequence or potential of repeated motifs to form alternative DNA structures. This suggests that in addition to nucleotide composition of repeat motifs, characteristic DNA replication/repair/recombination machinery might play an important role in the genesis of repeats. Moreover, analysis of complete genome coding DNA sequences of Drosophila, C. elegans, and yeast indicated that expansions of codon repeats corresponding to small hydrophilic amino acids are tolerated more, while strong selection pressures probably eliminate codon repeats encoding hydrophobic and basic amino acids. The locations and sequences of all of the repeat loci detected in genome sequences and coding DNA sequences are available at http://www.ncl-india.org/ssr and could be useful for further studies.

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

“…In plant ESTs, TNRs abundance in SSRs may be attributed to the absence of frame shift mutations within the transcribed genes which have resulted in the suppression of non-tri nucleotide SSRs in coding regions (Metzgar et al 2000). Among the TNRs, codon repeats correspond to small hydrophilic amino acids which have been easily tolerated than hydrophobic and basic amino acids (Katti et al 2001). Four thousand nine hundred and seventy eight (4978) codons were identified in castor EST-SSRs sequence data.…”

Searching microsatellites in DNA sequences: approaches used and tools developed

“…Compound microsatellites are identified by measuring the distance between the two microsatellites with distance equaling zero. The same approach was previously described in Sputnik, by Katti et al (2001) and Bilgen et al (2004). Imperfect Microsatellite Extractor (IMEx) allows harbouring k mismatches (point mutations) at each of the iterations due to indels or substitutions (Mudunuri and Nagarajaram 2007).…”

“…(Varshney et al 2005;Sharma et al 2007;Grover and Sharma 2011). However, the choice of microsatellite mining criteria and algorithms adopted for the purpose of screening genomic sequences for identifying microsatellites therein offer a lot of diversity (Toth et al 2000;Katti et al 2001;Dieringer and Schlotterer 2003;La Rota et al 2005). Each of the algorithm used in these studies fulfills a certain criteria and accordingly is based on a different principle.…”

Escherichia coli DNA polymerase IV contributes to spontaneous mutagenesis at coding sequences but not microsatellite alleles

“…Microsatellite sequences of 1-5 nucleotides per unit repeat are found throughout the human genome [1][2][3][4][5][6][7][8]. Microsatellite sequences are often hotspots for mutation, and an increase in mutagenesis is observed as the length of the repeated sequence increases [9,10].…”