Due mainly to large genome size and prevalence of repetitive sequences in the nuclear genome of spruce (
Picea
Mill.), it is very difficult to develop single-copy genomic microsatellite markers. We ...have developed and characterized 25 polymorphic, single-copy genic microsatellites from white spruce (
Picea glauca
(Moench) Voss) EST sequences and determined their informativeness in white spruce and black spruce (
Picea mariana
(Mill.) B.S.P.) and inheritance in black spruce. White spruce EST sequences from NCBI dbEST were searched for the presence of microsatellite repeats. Forty-seven sequences containing dinucleotide, trinucleotide, tetranucleotide and compound repeats were selected to develop primers. Twenty-five of the designed primer pairs yielded scorable amplicons, with single-locus patterns, and were characterized in 20 individuals each of white spruce and black spruce. All 25 microsatellites were polymorphic in white spruce and 24 in black spruce. The number of alleles at a locus ranged from two to 18, with a mean of 8.8 in white spruce, and from one to 17, with a mean of 7.6 in black spruce. The expected heterozygosity/polymorphic information content ranged from 0.10 to 0.92, with a mean of 0.67 in white spruce, and from 0 to 0.93, with a mean of 0.59 in black spruce. Microsatellites with dinucleotide and compound repeats were more informative than those with trinucleotide and tetranucleotide repeats. Eighteen microsatellite markers polymorphic between the parents of a black spruce controlled cross inherited in a single-locus Mendelian fashion. The microsatellite markers developed can be applied for various genetics, genomics, breeding, and conservation studies and applications
.
FIS multilocus 0,089. Relaciones genéticas con otras razas: FIS 0,059, FIT 0,178, FST 0,126, Número de migrantes 2,99 con la Berrenda Colorada. La mayor diferenciación genética con el GYR (0,239), la ...mayor distancia genética Gyr y Bramhan (0,273-0,234), en la estructura genética, las vacas CLT se diferenciaron del grupo de las demás razas en el Kluster 9. Los resultados muestran que se está ante una población con una gran diversidad genética, analizando la población de CLT con otras razas criollas, europeas y autóctonas españolas, se tiene una población que no tiene invasión de otras razas y que todavía tiene cierto grado de pureza, a excepción de cuatro animales que tienen cruces y perdieron la pureza de la raza.
El estudio de la estructura genética de las poblaciones Criollas es esencial para comprender el potencial evolutivo y la conectividad, para esto se han aplicado varios marcadores incluyendo isoenzimas, proteínas sanguíneas, fragmentos de ADN polimórfico amplificados al azar y microsatélites. El objetivo de esta investigación fue estudiar la variabilidad genética y la estructura de la población de un hato bovino de 45 vacas Criollo Lechero Tropical (CLT) pertenecientes a la Unidad de Manejo para la Conservación de la Vida Silvestre (UMA) “El Ravelo”, asimismo, establecer sus relaciones genéticas con otras razas europeas y criollas como referencia, utilizando microsatélites de ADN. El ADN se extrajo del pelo de cada uno de los animales, se utilizó un panel de 27 microsatélites recomendados por la FAO, se utilizaron los programas Genescan Analisys 3.1.2 y Genotyper 2.5 para la tipificación alélica. Para obtener el análisis genético se realizaron los análisis estadísticos de las frecuencias alélicas (FA), genotípicas, equilibrio Hardy-Weinberg (HW), Heterocigosis esperada (HE) y observada (HO), estadísticos F y GST, valores de Contenido de Información Polimórfica (PIC), distancias genéticas individuales y el estudio de la estructura población para identificar la conformación de esta población de Bovinos CLT. Las medias de los resultados de los análisis estadísticos: en las FA 7,36
effective number of alleles 3,837
número de alelos efectivos 3,837
Multilocus FIS 0.089. Genetic relationships with other races: FIS 0.059, 0.178 FIT, FST 0.126, 2.99, Number of migrants with Berrenda Colorada. Most genetic differentiation with GYR (0.239), the genetic distance Bramhan and Gyr (0.273 to 0.234) in the genetic structure, the CLT group cows differed from other breeds in the Kluster 9. The results show a population with a high variability and genetic diversity, the CLT population with Creoles of Spanish and European native breeds showed no mix of other breeds and have high purity, except for the 4 animals with influence from other cattle breeds.
The study of the genetic structure of populations Creole is essential for understanding the evolutionary potential and connectivity to other breeds. The objective of this research was to study the genetic variability and population structure of a bovine herd of 45 cows Tropical Milking Creole (CLT) also establish their genetic relationships with other European and reference landraces using microsatellite DNA. The DNA was extracted from hair and a panel of 27 microsatellite FAO recommended was used. Statistical genetic analysis was performed to allele frequencies (AF), genotypic, Hardy-Weinberg (HW), expected heterozygosity (HE) and observed (HO), F statistics and GST, Polymorphic Information Content (PIC), individual genetic distances and population structure to identify the formation of this population of cattle CLT. The means of the results of statistical analysis: the FA 7.36
los microsatelites mostraron desviaciones significativas por déficit de heterocigotos, HE 0,702 y HO de 0,639
HE, HO 0.702 and 0.639
Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for ...genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq).
Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-H
) was not significantly correlated with genome-wide SNP diversity estimates (SNP-H
and θ
) in A. halleri. Instead, microsatellite allelic richness (A
) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (F
) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genome-wide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation.
We recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to A. halleri, a few thousand SNPs are sufficient to achieve this goal.
Tumor mutational burden correlates with response to immune checkpoint blockade in multiple solid tumors, although in microsatellite-stable tumors this association is of uncertain clinical utility. ...Here we uniformly analyzed whole-exome sequencing (WES) of 249 tumors and matched normal tissue from patients with clinically annotated outcomes to immune checkpoint therapy, including radiographic response, across multiple cancer types to examine additional tumor genomic features that contribute to selective response. Our analyses identified genomic correlates of response beyond mutational burden, including somatic events in individual driver genes, certain global mutational signatures, and specific HLA-restricted neoantigens. However, these features were often interrelated, highlighting the complexity of identifying genetic driver events that generate an immunoresponsive tumor environment. This study lays a path forward in analyzing large clinical cohorts in an integrated and multifaceted manner to enhance the ability to discover clinically meaningful predictive features of response to immune checkpoint blockade.
Microsatellites, or Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes. Emerging evidence points to their role in cellular processes and gene regulation. ...Despite the huge resource of genomic information currently available, SSRs have been studied in a limited context and compared across relatively few species.
We have identified ~ 685 million eukaryotic microsatellites and analyzed their genomic trends across 15 taxonomic subgroups from protists to mammals. The distribution of SSRs reveals taxon-specific variations in their exonic, intronic and intergenic densities. Our analysis reveals the differences among non-related species and novel patterns uniquely demarcating closely related species. We document several repeats common across subgroups as well as rare SSRs that are excluded almost throughout evolution. We further identify species-specific signatures in pathogens like Leishmania as well as in cereal crops, Drosophila, birds and primates. We also find that distinct SSRs preferentially exist as long repeating units in different subgroups; most unicellular organisms show no length preference for any SSR class, while many SSR motifs accumulate as long repeats in complex organisms, especially in mammals.
We present a comprehensive analysis of SSRs across taxa at an unprecedented scale. Our analysis indicates that the SSR composition of organisms with heterogeneous cell types is highly constrained, while simpler organisms such as protists, green algae and fungi show greater diversity in motif abundance, density and GC content. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and for studying their roles across the evolutionary landscape.
Microsatellites are a ubiquitous occurrence in prokaryotic and eukaryotic genomes. Microsatellites have become one of the most popular classes of genetic markers due to their high reproducibility, ...multi-allelic nature, co-dominant mode of inheritance, abundance and wide genome coverage. We characterised microsatellites in the genomes and genes of two bat species, Pteropus vampyrus and Miniopterus natalensis. This characterisation was used for gene ontology analysis and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment of coding sequences (CDS).
Compared to M. natalensis, the genome size of P. vampyrus is larger and contains more microsatellites, but the total diversity of both species is similar. Mononucleotide and dinucleotide repeats were the most diverse in the genome of the two species. In each bat species, the microsatellite bias was obvious. The microsatellites with the largest number of repeat motifs in P. vampyrus from mononucleotide to hexanucleotide were (A)
, (AC)
, (CAA)
, (AAAC)
, (AACAA)
and (AAACAA)
, with frequencies of 97.94%, 58.75%, 30.53%, 22.82%, 54.68% and 22.87%, respectively, while in M. natalensis were (A)
, (AC)
, (TAT)
, (TTTA)
, (AACAA)
and (GAGAGG)
, with of 92.00%, 34.08%, 40.36%, 21.83%, 25.42% and 12.79%, respectively. In both species, the diversity of microsatellites was highest in intergenic regions, followed by intronic, untranslated and exonic regions and lowest in coding regions. Location analysis indicated that microsatellites were mainly concentrated at both ends of the genes. Microsatellites in the CDS are thus subject to higher selective pressure. In the GO analysis, two unique GO terms were found only in P. vampyrus and M. natalensis, respectively. In KEGG enriched pathway, the biosynthesis of other secondary metabolites and metabolism of other amino acids in metabolism pathways were present only in M. natalensis. The combined biological process, cellular components and molecular function ontology are reflected in the GO analysis and six functional enrichments in KEGG annotation, suggesting advantageous mutations during species evolution.
Our study gives a comparative characterization of the genomes of microsatellites composition in the two bat species. And also allow further study on the effect of microsatellites on gene function as well as provide an insight into the molecular basis for species adaptation to new and changing environments.
In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, ...characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation. To validate the accuracy of the findings, a sample of nine markers was subjected to in vitro testing, which confirmed the presence of polymorphisms within the population. These results suggest the existence of different protein isoforms within the population, indicating the potential of these markers for application in both population and phenotype-genotype association studies. This innovative approach opens up new possibilities for investigating the impact of genomic plasticity in populations of P. vannamei.
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