Simple sequence repeats as a source of quantitative genetic variation

Kashi, Yechezkel; King, David G.; Soller, M.

doi:10.1016/s0168-9525(97)01008-1

Cited by 415 publications

(276 citation statements)

References 73 publications

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“…The hypothesis connecting part of the SSR to pathogenicity is supported by the more frequent appearance (per megabase) of L-SSR and of MNR (Ͼ8 bp) in chromosome 1 (Table 2), which carries more genes associated with pathogenicity than does chromosome 2 (32). Polymorphism at SSR tracts could have a functional role affecting both gene regulation and the expressed protein, such that this variation could become available for natural selection and subsequent evolution (36,37,42,57). SSR polymorphism, found in regulatory regions of bacterial species, was found to be associated with variation in gene expression (i.e., on-off switches and levels), providing the dynamic response to environmental changes (4,52,56) [see the discussion of the VC1457- (7) could have various biological effects (Table 3) (41).…”

Section: Discussionmentioning

confidence: 99%

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

et al. 2007

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Vibrio cholerae is the etiological agent of cholera. Its natural reservoir is the aquatic environment. To date, practical typing of V. cholerae is mainly serological and requires about 200 antisera. Simple sequence repeats (SSR), also termed VNTR (for variable number of tandem repeats), provide a source of high genomic polymorphism used in bacterial typing. Here we describe an SSR-based typing method that combines the variation in highly mutable SSR loci, with that of shorter, relatively more stable mononucleotide repeat (MNR) loci, for accurate and rapid typing of V. cholerae. Vibrio cholerae, a gram-negative bacterium, is the causal agent of the severe diarrheal disease cholera. Its natural reservoir is the aquatic environment (49, 84). Cholera pandemics are caused by specific serogroups of V. cholerae that are pathogenic only to humans (35,84). Since 1817, V. cholerae has caused a number of pandemics. The first seven were presumed to be caused by O1 serogroup of V. cholerae (68). In October 1992, a new serogroup, defined O139, caused a severe outbreak of cholera in southeast India. Within 10 months, the O139 serogroup was disseminated all over the Indian subcontinent and soon thereafter spread to 11 neighboring countries, temporarily displacing the O1 serogroups (64). Since then both serogroups coexist and are responsible for large outbreaks. Genomic studies indicated that O139 epidemic strain arose by horizontal acquisition of unique DNA (15, 47).Traditionally, V. cholerae classification is serological and requires about 200 antisera based on the somatic O antigen (72). Isolates of V. cholerae are divided into three major subgroups: O1, O139, and non-O1/non-O139, of which only the O1 and O139 serogroups are associated with cholera pandemics and epidemics. Non-O1, non-O139 serogroups are recognized as causative agents of sporadic and localized outbreaks (73). Pathogenic V. cholerae isolates carry virulence genes, such as the toxins genes ctxAB (25,65,68). The environmental V. cholerae strains from non-O1, non-O139 serogroups are a possible natural reservoir of potentially new emerging epidemic strains (67,73). This assumption is supported by the finding that some of these environmental strains harbor virulence genes (23) and thus are likely to evolve into novel pathogenic strains by horizontal gene transfer (24,25). The emergence of new pathogenic V. cholerae strains requires not only an efficient, rapid, and accurate identification tool but also a means for determining genetic relationships among environmental and clinical isolates.Genome-based bacterial identification and typing is essential for several disciplines, including taxonomy, epidemiology, determining phylogenetic relationships, and the study of evolutionary mechanisms. It allows distinguishing among strains within a species to monitor epidemics and routes of contamination. Recent advances in biotechnology have resulted in the development of numerous methods for microorganism typing that differ in their sensitivity, rapidity, complexity, discrimin...

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Section: Discussionmentioning

confidence: 99%

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

et al. 2007

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“…Di-nucleotide repeats are more prevalent than trinucleotide repeats due to instability of dinucleotide repeats because of higher slippage rate (35). The repeat sequences may provide a molecular device for faster adaptation to environmental stresses (9,19,36); thus may accelerate the evolution of the Filoviridae family.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

2015

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Background:Microsatellites have evoked the interest of researchers owing to their applications in different fields such as DNA fingerprinting, genetic mapping, population genetics, forensics, paternity studies and evolution. Objectives: The present study focused on the analysis of simple sequence repeats (SSRs) in genomes of seven species from three genera of the Filoviridae family. Materials and Methods: Genome sequences of seven species from the Filoviridae family were assessed by the National Center for Biotechnology Information (NCBI), microsatellites were extracted using the IMEx software, and statistical analysis was performed Microsoft Office Excel 2007. Results: A total of 516 microsatellites and 14 Compound Simple Sequence Repeats (cSSR) (also known as compound microsatellites) were extracted. Evidently, the conversion of SSRs to cSSR was low. Mononucleotide A/T was the most prevalent followed by dinucleotide AC/CA and trinucleotide AAC/CAA. Highest incidence of SSRs (mon-/di-nucleotide motif) was observed in RNA Dependent RNA Polymerase (RDRP) gene whereas tri-nucleotide motif was maximally localized in nucleoproteins (NP). Conclusions:The salient features of simple and compound microsatellites in Filoviridae family have been highlighted herein. Microsatellite regions with higher mutation rates compared to the rest of the genome play a crucial role in genome evolution by acting as a source of quantitative genetic variation. The SSR mutation rate is known to be affected by motif length, motif sequence, and number of repeats and purity of repetition. The functional role of tandem repeats in viruses, remains to be fully elucidated. However, with the repetitive sequence allegedly acting as a hot spot for recombination, we postulate their involvement in genetic events such as recombination, replication, and repair mechanisms that drive sequence diversity leading to the formation of the genetic basis of adaptation.

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“…Occurrence of SSRs in the promoter region influences transcriptional activity (Kashi et al, 1997), whereas their presence in non coding regions influences gene regulation, transcription (Martin et al, 2004;Lawson and Zhang, 2006) and recombination events (Bagshaw et al, 2008). The over-representation of CT/GA and CTT/GAA repeats in the 5'-flanks of Arabidopsis thaliana suggest their potential involvement in regulating gene expression .…”

Section: Microsatellites and Their Influence On Molecular Functionsmentioning

confidence: 99%

Methods for Development of Microsatellite Markers: An Overview

et al. 2014

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Microsatellite or Simple Sequence Repeat (SSR) markers have evolved to the status of a most versatile and popular genetic marker in a ubiquity of plant systems. Due to their co-dominant, hyper-variable and multiallelic nature, they are the prominent markers of choice for fingerprinting, conservation genetics, plant breeding and phylogenetic studies. Despite its development of a new set of SSR markers for a species remained time consuming and expensive for many years. However, with the recent advancement in genomics, new strategies/protocols are now available for the generation of SSR markers. This review presents an overview on microsatellite markers with a special emphasis on the various strategies used for the development of microsatellite markers.

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Simple sequence repeats as a source of quantitative genetic variation

Cited by 415 publications

References 73 publications

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

Methods for Development of Microsatellite Markers: An Overview

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