Association of microsatellite pairs with segmental duplications in insect genomes

BMC Genomics
Susanta K Behura, David W Severson

Abstract

Segmental duplications (SDs), also known as low-copy repeats, are DNA sequences of length greater than 1 kb which are duplicated with a high degree of sequence identity (greater than 90%) causing instability in genomes. SDs are generally found in the genome as mosaic forms of duplicated sequences which are generated by a two-step process: first, multiple duplicated sequences are aggregated at specific genomic regions, and then, these primary duplications undergo multiple secondary duplications. However, the mechanism of how duplicated sequences are aggregated in the first place is not well understood. By analyzing the distribution of microsatellite sequences among twenty insect species in a genome-wide manner it was found that pairs of microsatellites along with the intervening sequences were duplicated multiple times in each genome. They were found as low copy repeats or segmental duplications when the duplicated loci were greater than 1 kb in length and had greater than 90% sequence similarity. By performing a sliding-window genomic analysis for number of paired microsatellites and number of segmental duplications, it was observed that regions rich in repetitive paired microsatellites tend to get richer in segmental duplicati...Continue Reading

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Citations

Oct 27, 2016·Molecular Genetics and Genomics : MGG·Juan Pablo Isaza, Juan Fernando Alzate

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Datasets Mentioned

BETA
AY119274

Software Mentioned

Ensembl Metazoa
R
R package ‘ Biostrings ’
SciRoKo
R package SeqINR
MEGA4
DnaSP

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