scholarly journals Simple Sequence Repeats and Genome Plasticity in Streptococcus agalactiae

2010 ◽  
Vol 192 (15) ◽  
pp. 3990-4000 ◽  
Author(s):  
Robert Janulczyk ◽  
Vega Masignani ◽  
Domenico Maione ◽  
Hervé Tettelin ◽  
Guido Grandi ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Streptococcus Agalactiae ◽  
Antigenic Variation ◽  
Phase Variation ◽  
Open Reading Frames ◽  
Genome Plasticity ◽  
Gram Negative ◽  
Ssr Loci ◽  
Gram Negative Organisms ◽  
Simple Sequence

ABSTRACT Simple sequence repeats (SSRs) and their role in phase variation have been extensively studied in Gram-negative organisms, where they have been associated with antigenic variation and other adaptation strategies. In this study, we apply comparative genomics in order to find evidence of slipped-strand mispairing in the human Gram-positive pathogen Streptococcus agalactiae. In two consecutive screenings, 2,233 (650 + 1,583) SSRs were identified in our reference genome 2603V/R, and these loci were examined in seven other S. agalactiae genomes. A total of 56 SSR loci were found to exhibit variation, where gain or loss of repeat units was observed in at least one other genome, resulting in aberrant genotypes. Homopolymeric adenine tracts predominated among the repeats that varied. Positional analysis revealed that long polyadenine tracts were overrepresented in the 5′ ends of open reading frames (ORFs) and underrepresented in the 3′ ends. Repeat clustering in ORFs was also examined, and the highest degree of clustering was observed for a capsule biosynthesis gene and a pilus sortase. A statistical analysis of observed over expected ratios suggested a selective pressure against long homopolymeric tracts. Altered phenotypes were verified for three genes encoding surface-attached proteins, in which frameshifts or fusions led to truncation of proteins and/or affected surface localization through loss or gain of the cell wall sorting signal. The data suggest that SSRs contributes to genome plasticity in S. agalactiae but that the bet-hedging strategy is different from Gram-negative organisms.

scholarly journals Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

scholarly journals Identification of Simple-sequence Repeats in Malus (Apple)

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 855D-855 ◽  
Author(s):  
Amy K. Szewc-McFadden ◽  
Sharon Bliek ◽  
Christopher G. Alpha ◽  
Warren F. Lamboy ◽  
James R. McFerson
Keyword(s):  
Simple Sequence Repeats ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Germplasm Characterization ◽  
The Core ◽  
Marker Data ◽  
Core Subset ◽  
Germplasm Collections ◽  
Ssr Loci ◽  
Simple Sequence

Simple-sequence repeats (SSRs) are efficient and informative DNA markers with great potential for germplasm characterization. When used to characterize large arrays of accessions, such as the core subset of the USDA/ARS Malus collection, SSRs may be more effective than other approaches, such as restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD). For example, SSRs can be PCR-amplified and fluorescence-based detected; they also appear to be abundantly disbursed throughout plant genomes and yield abundant polymorphisms in most taxa studied. We are conducting an extensive screening of a size-fractionated library of Malus ×domestica cv. Golden Delicious to identify and characterize selected SSR loci. We are applying genetic information revealed by SSR loci in combination with passport and horticultural data to better comprehend genetic identity and relatedness in Malus germplasm collections and help develop the Malus core subset. Ultimately, application of molecular marker data will permit improved conservation and use of genetic resources.

scholarly journals Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 143
Author(s):  
Lei Zhu ◽  
Huayu Zhu ◽  
Yanman Li ◽  
Yong Wang ◽  
Xiangbin Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Motif Length ◽  
Pair Group ◽  
Ssr Loci ◽  
Ssr Frequency ◽  
Basic And Applied Research ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

scholarly journals Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

2020 ◽  
Author(s):  
Lei Zhu ◽  
Hua yu Zhu ◽  
Yan man Li ◽  
Xiang bin Wu ◽  
Jin tao Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomics ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Diversity Analysis ◽  
Motif Length ◽  
Genetic Diversity Analysis ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Background The Cucurbita genus contains important economic crops in the world, while limited molecular markers have been developed in the past years. Simple sequence repeats (SSR) markers are powerful tools for the study of genetic mapping construction, genetic diversity analysis and genome wide association. The availability of pumpkin genome information has made it possible to analyze SSRs in genome wide across three Cucurbita species. Results In this paper, based on the whole genome sequences, 34,375 SSR loci were found in C. moschata, 30,577 SSR loci were found in C. maxima and 38,104 SSR loci were found in C. pepo. C. pepo has the maximum density of SSRs with an average of 145 SSR/Mb. In general, the frequency in total SSR loci decreased with the increase of the motif length, dinucleotide motifs were the most common motifs in the three species, and for the same repeat types, the SSR frequency decreased sharply with the increase of the repeat number. Most of those SSR loci were suitable for marker development (84.75% in C. moscata, 94.53% in C. maxima and 95.09% in C. pepo). Based on those markers, we compared and analyzed the cross-species SSR markers between C. pepo and other Cucurbitaceae species by silico-PCR. Using these cross-species primers, the high collinear relationships between C. pepo and the other two species were detected, respectively. Furthermore, the application of SSR markers in genetic diversity analysis was tested in C. pepo, the results showed that they were good tools to be used in genetic diversity analysis. Conclusion In this study, the genome wide SSR markers were detected from three Cucurbita species, and some of their applications were proved by comparative genomics and genetic diversity analysis. The large number of genome-wide SSR markers and crossspecies markers would promote the basic and applied studies of Cucurbita species, such as gene mapping, QTLs mapping, comparative genomics and marker-assisted breeding.

scholarly journals Molecular polymorphism in SSR loci of the RB92579 variety: perspectives for use in sugarcane improvement and industrial sector

2020 ◽  
pp. 729-738
Author(s):  
Rodrigo Desordi ◽  
Claudete Aparecida Mangolin ◽  
Gustavo Barizon Maranho ◽  
Rone Charles Maranho ◽  
Maria de Fátima Pires da Silva Machado
Keyword(s):  
Simple Sequence Repeats ◽  
Genetic Divergence ◽  
Agricultural Productivity ◽  
Dna Amplification ◽  
Industrial Sector ◽  
Sugarcane Variety ◽  
Mato Grosso ◽  
South Central ◽  
Ssr Loci ◽  
Simple Sequence

The sugarcane variety RB92579 has excellent agricultural productivity, very low flowering, efficient water use, and a high content of sucrose. Despite its excellent agricultural productivity, the RB92579 has not been used as a direct parent in sugarcane improvement. The main goal of the present study was to investigate polymorphisms at the SSR and EST-SSR loci of the RB92579 sugarcane variety to evaluate its potential for breeding and generating new varieties and to guide better use by the industrial sector. A total of 92 samples of the RB92579 variety were collected from plants in the fourth cutting stage grown in two Brazilian states: Paraná (PR; South region) and Mato Grosso do Sul (MS; South-Central region). Four primers for DNA simple sequence repeats (SSRs) and eight primers for expressed sequence tags for simple sequence repeats (EST-SSR) were used for DNA amplification. The polymorphism occurrence in the 12 SSR loci was 28% in the PR and MS populations, with a total of 25 alleles and an average of 2.08 alleles/loci. High values for mean observed heterozygosity, a high value for genetic identity and a low level of population differentiation was found in samples from the PR and MS states. The number of polymorphisms in the EST-SSR and noncoding SSR loci as well as the genetic divergence was low. However, the high heterozygosity in both populations indicates that the RB92579 variety can be used as a parent to generate new cultivars. On the other hand, the low coefficient of genetic divergence and high identity coefficient indicate that there is genetic uniformity; therefore, there is no need for differential industrial adaptations for pretreatment or enzymatic hydrolysis of the sugarcane bagasse from RB92579 at the same cutting stage and planted in the two regions (PR and MS).

A Low Mutation Rate For Chloroplast Microsatellites

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 943-947
Author(s):  
Jim Provan ◽  
Nicole Soranzo ◽  
Neil J Wilson ◽  
David B Goldstein ◽  
Wayne Powell
Keyword(s):  
Chloroplast Genome ◽  
Mutation Rate ◽  
Simple Sequence Repeats ◽  
Mutation Rates ◽  
Chloroplast Microsatellites ◽  
Ssr Loci ◽  
Nuclear Ssr ◽  
Monomorphic Population ◽  
Simple Sequence ◽  
Pinus Torreyana

Abstract We used chloroplast simple sequence repeats (cpSSRs) to examine whether there is any variation present in the chloroplast genome of Pinus torreyana (Parry ex Carrière) that may previously not have been detected using RFLPs. Analysis of 17 cpSSR loci showed no variation, which is consistent with previous cpRFLP work and confirms that the species is descended from an original, highly monomorphic population following a bottleneck. This lack of biological variation in the chloroplast genome of P. torreyana allowed us to estimate the mutation rates at cpSSR loci as between 3.2 × 10-5 and 7.9 × 10-5. This estimate is lower than published mutation rates at nuclear SSR loci but higher than substitution rates elsewhere in the chloroplast genome.

scholarly journals Broad Conditions Favor the Evolution of Phase-Variable Loci

mBio ◽  
2013 ◽  
Vol 4 (1) ◽  
Author(s):  
M. E. Palmer ◽  
M. Lipsitch ◽  
E. R. Moxon ◽  
C. D. Bayliss
Keyword(s):  
Haemophilus Influenzae ◽  
In Silico ◽  
Simple Sequence Repeat ◽  
Phase Variation ◽  
Phase Variable ◽  
Infection Cycle ◽  
Sequence Repeat ◽  
Ssr Loci ◽  
Stochastic Switching ◽  
Simple Sequence

ABSTRACT Simple sequence repeat (SSR) tracts produce stochastic on-off switching, or phase variation, in the expression of a panoply of surface molecules in many bacterial commensals and pathogens. A change to the number of repeats in a tract may alter the phase of the translational reading frame, which toggles the on-off state of the switch. Here, we construct an in silico SSR locus with mutational dynamics calibrated to those of the Haemophilus influenzae mod locus. We simulate its evolution in a regimen of two alternating environments, simultaneously varying the selection coefficient, s, and the epoch length, T. Some recent work in a simpler (two-locus) model suggested that stochastic switching in a regimen of two alternating environments may be evolutionarily favored only if the selection coefficients in the two environments are nearly equal (“symmetric”) or selection is very strong. This finding was puzzling, as it greatly restricted the conditions under which stochastic switching might evolve. Instead, we find agreement with other recent theoretical work, observing selective utility for stochastic switching if the product sT is large enough for the favored state to nearly fix in both environments. Symmetry is required neither in s nor in sT. Because we simulate finite populations and use a detailed model of the SSR locus, we are also able to examine the impact of population size and of several SSR locus parameters. Our results indicate that conditions favoring evolution and maintenance of SSR loci in bacteria are quite broad. IMPORTANCE Bacteria experience frequent changes of environment during the infection cycle. One means to rapidly adapt is stochastic switching: a bacterial lineage will stochastically produce a variety of genotypes, so that some descendants will survive if the environment changes. Stochastic switching mediated by simple sequence repeat (SSR) loci is widespread among bacterial commensals and pathogens and influences critical interactions with host surfaces or immune effectors, thereby affecting host persistence, transmission, and virulence. Here, we use the most detailed in silico model of an SSR locus to date, with its phase variation calibrated to match the mod locus of Haemophilus influenzae. The type III restriction-modification system encoded by mod participates in the regulation of multiple other genes; thus, SSR-mediated phase variation of mod has far-reaching cis-regulatory effects. This coupling of phase-variable switching to complex phenotypic effects has been described as the “phasevarion” and is central to understanding the infection cycle of bacterial commensals and pathogens.

Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai)

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 433-441 ◽  
Author(s):  
R. L. Jarret ◽  
L. C. Merrick ◽  
T. Holms ◽  
J. Evans ◽  
M. K. Aradhya
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Genetic Relatedness ◽  
Genomic Library ◽  
Citrullus Lanatus ◽  
Dinucleotide Repeats ◽  
Length Polymorphisms ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total of 96 (0.53%) SSR-bearing clones were identified and the inserts from 50 of these were sequenced. The dinucleotide repeats (CT)n and (GA)n accounted for 82% of the SSRs sequenced. PCR primer pairs flanking seven SSR loci were used to amplify SSRs from 32 morphologically variable watermelon genotypes from Africa, Europe, Asia, and Mexico and a single accession of Citrullus colocynthis from Chad. Cluster analysis of SSR length polymorphisms delineated 4 groups at the 25% level of genetic similarity. The largest group contained C. lanatus var. lanatus accessions. The second largest group contained only wild and cultivated "citron"-type or C. lanatus var. citroides accessions. The third group contained an accession tentatively identified as C. lanatus var. lanatus but which perhaps is a hybrid between C. lanatus var. lanatus and C. lanatus var. citroides. The fourth group consisted of a single accession identified as C. colocynthis. "Egusi"-type watermelons from Nigeria grouped with C. lanatus var. lanatus. The use of SSRs for watermelon germplasm characterization and genetic diversity studies is discussed.Key words: Citrullus, watermelon, simple sequence repeats, genetic diversity.

scholarly journals Mining of Simple Sequence Repeats Loci, Genetic Relationship And Population Structure of Bottle Gourd (Lagenaria Siceraria (Molina) Standl.) Accessions With Different Geographical Origin Using Single Nucleotide Polymorphism (SNPs) Markers

2021 ◽  
Author(s):  
Rodrigo Iván Contreras-Soto ◽  
Ariel Salvatierra ◽  
Carlos Maldonado ◽  
Jacob Mashilo
Keyword(s):  
South Africa ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Simple Sequence Repeats ◽  
Bottle Gourd ◽  
Lagenaria Siceraria ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Lagenaria siceraria (Molina) Standl. (2n = 2x = 22) is an important horticultural and medicinal crop grown worldwide serving for food and pharmaceutical industries. The crop exhibit extensive phenotypic and genetic variation useful for cultivar obtention targeting economic traits, however limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd prevenient from Chile, Asia, and South Africa by using single nucleotide polymorphism (SNPs) markers and mining of simple sequence repeats (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs molecular markers classified as moderate to highly informative with mean polymorphic information content of 0.29. The mean gene diversity of 0.16, indicated low genetic differentiation of the accessions. Analysis of molecular variance revealed lower differentiation between (36%) than within (48%) bottle gourd accessions suggesting that random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising of South Africa accessions and an admixed group with genotypes of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

scholarly journals Sweetpotato Genome Fingerprinting and Parental Analysis Using Microsatellites.

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 612a-612
Author(s):  
Mario I. Buteler ◽  
Don R. LaBonte ◽  
Robert L. Jarret
Keyword(s):  
Simple Sequence Repeats ◽  
Silver Staining ◽  
Software Package ◽  
Reaction Products ◽  
Allelic Profile ◽  
Multiple Loci ◽  
Ssr Loci ◽  
Parental Analysis ◽  
Flat Bed Scanner ◽  
Simple Sequence

Microsatellites or simple sequence repeats (SSRs) were used to characterize 20 sweetpotato genotypes and to assign paternity for offspring from crosses among them. The PCR amplifications were performed with each of the sweetpotato genotypes and primers flanking a SSR loci previously characterized with the varieties Beauregard and Excel and 20 offspring from a cross among them. The PCR reaction products were separated in nondenaturing 12% acrylamide gels run at 25 V·cm–1 for 5 hours, and DNA fragments were visualized with silver staining. Gels were scanned on a flat bed scanner and analyzed using the Pro-RFLP software package. Three primer pairs were sufficient to produce an allelic profile capable of differentiating the 20 genotypes from each other. More than seven alleles/loci were found using each of the three primer pairs assayed. Occasionally primers produced allelic products clearly localized in two or three regions of the gel. These multiple loci segregated independently in a diploid fashion. This evidence suggests that there is not total homology among the three sweetpotato genomes.

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