Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review

Li, Youchun; Korol, Abraham B.; Fahima, Tzion; Beiles, Avigdor; Nevo, Eviatar

doi:10.1046/j.1365-294x.2002.01643.x

Cited by 984 publications

(827 citation statements)

References 149 publications

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“…They are generally found in nuclear genome, usually in non-coding parts of genome. Microsatellites are "junk" DNA, and are selectively neutral (Li et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Genetic Characterization of Albanian Sheep Breeds by Microsatellite Markers

Hoda¹,

Marsan²

2012

Analysis of Genetic Variation in Animals

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“…They are generally found in nuclear genome, usually in non-coding parts of genome. Microsatellites are "junk" DNA, and are selectively neutral (Li et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Genetic Characterization of Albanian Sheep Breeds by Microsatellite Markers

Hoda¹,

Marsan²

2012

Analysis of Genetic Variation in Animals

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“…Parallel to the rapid increase in availability of diverse DNA sequence data, which resulted from the huge advancement of sequencing techniques, labour-intensive methods for the generation of microsatellite markers have been replaced gradually by in silico data mining of genomic and expressed sequence tag (EST) datasets [19-21]. Microsatellites are effectively randomly distributed throughout the genome and can represent transcribed elements.…”

Section: Introductionmentioning

confidence: 99%

Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)

Hamarsheh

Amro

2011

Parasites Vectors

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BackgroundPhlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs), or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers.ResultsSimple sequence repeats (SSRs) were characterized in P. papatasi expressed sequence tags (ESTs) derived from a public database, National Center for Biotechnology Information (NCBI). A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AX)n repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation.ConclusionThe first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

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“…For example, a potentially large number of microsatellites could be developed inexpensively through mining D. v. virgifera expressed sequence tag (EST) databases (Kim et al 2008). Although EST-derived microsatellites loci are part of an expressed gene and thus may be subject to direct selection, background selection, or genetic hitchhiking (Li et al 2002), polymorphisms in EST-derived microsatellites often behave as effectively neutral markers and can provide valid information about the genetic structure of natural populations (Woodhead et al 2005, Kim et al 2008.…”

Section: Discussionmentioning

confidence: 99%