Mining microsatellites in eukaryotic genomes

Sharma, Prakash C.; Grover, Atul; Kahl, Günter

doi:10.1016/j.tibtech.2007.07.013

Cited by 231 publications

(209 citation statements)

References 54 publications

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“…When the same genome was scanned with the same tool by default parameters, this proportion was raised to 3.9% (International Human Genome Sequencing Consortium 2001). Further, Sharma et al (2007) used MISA to obtain a value~1% in the same genome. Thus, a good practice would be to use more than one tool and find the common set of microsatellites detected by the two.…”

Section: Microsatellite Search Approaches and Tools: User's Perspectivementioning

confidence: 99%

“…Stochastic models Microsatellites, also known as Simple Sequence Repeats (SSRs), represent specific sequences in genomic DNA composed of short motifs (typically 1-6 bp) repeated for many number of times. Such sequences are abundant and distributed all over the eukaryotic genomes with variable frequency (Sharma et al 2007;Guo et al 2009). Higher rates of mutations at these loci (Eckert and Hile 2009) compared to other regions of genomic DNA, often generate inter-and intra-specific genetic variation (Agarwal et al 2008), allowing their wide exploitation as genetic markers.…”

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confidence: 99%

“…Such methods have been found to be extremely successful in molecular marker development for the purpose of gene tagging, marker assisted selection, molecular mapping, etc. (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).…”

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confidence: 99%

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Searching microsatellites in DNA sequences: approaches used and tools developed

Grover

Aishwarya

Sharma

2011

Physiol Mol Biol Plants

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Microsatellite instability associated genomic activities and evolutionary changes have led to a renewed focus on microsatellite research. In last decade, a number of microsatellite mining tools have been introduced based on different computational approaches. The choice is generally made between slow but exhaustive dynamic programming based approaches, or fast and incomplete heuristic methods. Tools based on stochastic approaches are more popular due to their simplicity and added ornamental features. We have performed a comparative evaluation of the relative efficiency of some microsatellite search tools with their default settings. The graphical user interface, the statistical analysis of the output and ability to mine imperfect repeats are the most important criteria in selecting a tool for a particular investigation. However, none of the available tools alone provides complete and accurate information about microsatellites, and a lot depends on the discretion of the user.

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Section: Microsatellite Search Approaches and Tools: User's Perspectivementioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Searching microsatellites in DNA sequences: approaches used and tools developed

Grover

Aishwarya

Sharma

2011

Physiol Mol Biol Plants

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“…Ten motifs most commonly found in this study were (GAA) 2 , (C) 6 , (CG) 3 , (A) 6 , (TGG) 2 T, (G) 6 , (TGC) 2 , (GTT) 2 G, and (C) 7 , as many as 52 , 43, 34, 23, 21, 21, 20, 20, 19, and 18 sequentially. If the motifs were grouped based on repeat perfection (Weber, 1990;Sharma, Grover, & Kahl, 2007), it was found 217 perfect, 121 imperfect, 25 perfect compound, and 71 imperfect compound motifs. In general, single motif found from durian genomic library has short repeat size (<10 nt) which reached 328 (89.6 %), whilst longer size varies from 11 to 89 nt were found only 38 (10.4 %) motifs.…”

Section: Ssr Motifs and Primer Designmentioning

confidence: 99%

“…Microsatellite motifs could be obtained through in silico technique for crops that are already available their genomic data base, or through isolation from genomic library for those which their data base are not available yet (Sharma, Grover, & Kahl, 2007). The number of durian SSR loci listed in GeneBank, so far, is very limited.…”

Section: Introductionmentioning

confidence: 99%

Development of Simple-Sequence Repeats Markers from Durian (Durio zibethinus Murr. cultv. Matahari) Genomic Library

Santoso¹,

Pancoro²,

Suhandono³

et al. 2017

Agrivita.J.Agr.Sci

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Simple sequence repeats have been proved as powerful markers and widely used in molecular breeding to reduce cycles and cost efective. The availability of the marker is, however, very limited in durian. This research aimed to develop SSR markers from durian genomic library. Genomic DNA was isolated from durian shoot leaf, whilst SSR motifs were isolated using membrane-based oligonucleotide enrichment hybridization protocol. Annotation made on the library found 527 unique motifs from 354 durian libraries which form 425 loci. The SSR motifs obtained were generally short repeats which reached 89.6 %, whilst longer repeats were found consisted of compound motifs. Eleven loci were selected as representative for further test to prove their informativity. A number of unique allels were successfully amplified from 17 durian genomes. The analysis showed the polymorphic information content (PIC) values ranged from 0.000 to 0.662 with an average of 0.390. The SSR loci also showed their ability to be used for durian diversity analysis as the evident that the loci could be used as genetic markers for assisting further durian breeding program.

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