An Analysis of Microsatellite Loci in Arabidopsis thaliana: Mutational Dynamics and Application

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1475-1488
Author(s):  
V Vaughan Symonds ◽  
Alan M Lloyd
Keyword(s):  
Arabidopsis Thaliana ◽  
Microsatellite Loci ◽  
Current Knowledge ◽  
Flowering Plant ◽  
Allele Frequency Distribution ◽  
Strongly Correlated ◽  
Microsatellite Evolution ◽  
Stepwise Mutation ◽  
Mutation Pattern ◽  
Infinite Alleles Model

Abstract Microsatellite loci are among the most commonly used molecular markers. These loci typically exhibit variation for allele frequency distribution within a species. However, the factors contributing to this variation are not well understood. To expand on the current knowledge of microsatellite evolution, 20 microsatellite loci were examined for 126 accessions of the flowering plant, Arabidopsis thaliana. Substantial variability in mutation pattern among loci was found, most of which cannot be explained by the assumptions of the traditional stepwise mutation model or infinite alleles model. Here it is shown that the degree of locus diversity is strongly correlated with the number of contiguous repeats, more so than with the total number of repeats. These findings support a strong role for repeat disruptions in stabilizing microsatellite loci by reducing the substrate for polymerase slippage and recombination. Results of cluster analyses are also presented, demonstrating the potential of microsatellite loci for resolving relationships among accessions of A. thaliana.

scholarly journals Microsatellite evolution in sunfish (Centrarchidae)

1999 ◽  
Vol 56 (7) ◽  
pp. 1198-1205 ◽  
Author(s):  
Bryan D Neff ◽  
Peng Fu ◽  
Mart R Gross
Keyword(s):  
Microsatellite Loci ◽  
Micropterus Salmoides ◽  
Lepomis Macrochirus ◽  
Sequence Divergence ◽  
Mendelian Inheritance ◽  
Lepomis Gibbosus ◽  
Microsatellite Evolution ◽  
Stepwise Mutation ◽  
Flanking Sequences ◽  
Infinite Alleles Model

We describe 10 microsatellite loci from bluegill (Lepomis macrochirus) and discuss their evolution within the Centrarchidae. All of the loci exhibit Mendelian inheritance and are unlinked. While six loci are conserved within the Centrarchidae (found also in pumpkinseed (Lepomis gibbosus) and largemouth bass (Micropterus salmoides)), four have origins outside the family and two predate it by 65-150 million years. The persistence of these loci in fish may be due to a slow rate of sequence divergence within their flanking sequences, estimated at 0.14-0.83% per million years. We examine the number of alleles, heterozygosity, range, modes, and the frequency of the most common allele and find that a two-phased model (TPM) or an infinite alleles-model (IAM) best describes the results, while a stepwise mutation model (SMM) is rejected. Therefore, population differentiation analyses utilizing these microsatellite loci should consider parameters based on the IAM (e.g., FST) and not the SMM.

scholarly journals Evidence for Complex Mutations at Microsatellite Loci in Drosophila

Genetics ◽  
1999 ◽  
Vol 152 (2) ◽  
pp. 617-627 ◽  
Author(s):  
Isabelle Colson ◽  
David B Goldstein
Keyword(s):  
Microsatellite Loci ◽  
Size Variation ◽  
Strongly Correlated ◽  
Sequence Structure ◽  
Repeat Array ◽  
Stepwise Mutation ◽  
Mutation Pattern ◽  
Microsatellite Mutation ◽  
Repeat Count ◽  
Selection Of

Abstract Fifteen lines each of Drosophila melanogaster, D. simulans, and D. sechellia were scored for 19 microsatellite loci. One to four alleles of each locus in each species were sequenced, and microsatellite variability was compared with sequence structure. Only 7 loci had their size variation among species consistent with the occurrence of strictly stepwise mutations in the repeat array, the others showing extensive variability in the flanking region compared to that within the microsatellite itself. Polymorphisms apparently resulting from complex nonstepwise mutations involving the microsatellite were also observed, both within and between species. Maximum number of perfect repeats and variance of repeat count were found to be strongly correlated in microsatellites showing an apparently stepwise mutation pattern. These data indicate that many microsatellite mutation events are more complex than represented even by generalized stepwise mutation models. Care should therefore be taken in inferring population or phylogenetic relationships from microsatellite size data alone. The analysis also indicates, however, that evaluation of sequence structure may allow selection of microsatellites that more closely match the assumptions of stepwise models.

scholarly journals An evaluation of genetic distances for use with microsatellite loci.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 463-471 ◽  
Author(s):  
D B Goldstein ◽  
A Ruiz Linares ◽  
L L Cavalli-Sforza ◽  
M W Feldman
Keyword(s):  
Microsatellite Loci ◽  
Phylogenetic Reconstruction ◽  
Genetic Distances ◽  
Stepwise Mutation Model ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
The Difference ◽  
Nei's Distance ◽  
Infinite Alleles Model ◽  
Overall Reliability

Abstract Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

scholarly journals The Role of Major Histocompatibility Complex in Organ Transplantation- Donor Specific Anti-Major Histocompatibility Complex Antibodies Analysis Goes to the Next Stage -

2019 ◽  
Vol 20 (18) ◽  
pp. 4544 ◽  
Author(s):  
Tsukasa Nakamura ◽  
Takayuki Shirouzu ◽  
Katsuya Nakata ◽  
Norio Yoshimura ◽  
Hidetaka Ushigome
Keyword(s):  
Major Histocompatibility Complex ◽  
Organ Transplantation ◽  
Current Knowledge ◽  
Human Leukocyte ◽  
Strongly Correlated ◽  
Human Beings ◽  
Major Histocompatibility ◽  
Antibody Mediated Rejection ◽  
Leukocyte Antigens ◽  
Histocompatibility Complex

Organ transplantation has progressed with the comprehension of the major histocompatibility complex (MHC). It is true that the outcome of organ transplantation largely relies on how well rejection is managed. It is no exaggeration to say that to be well acquainted with MHC is a shortcut to control rejection. In human beings, MHC is generally recognized as human leukocyte antigens (HLA). Under the current circumstances, the number of alleles is still increasing, but the function is not completely understood. Their roles in organ transplantation are of vital importance, because mismatches of HLA alleles possibly evoke both cellular and antibody-mediated rejection. Even though the control of cellular rejection has improved by recent advances of immunosuppressants, there is no doubt that antibody-mediated rejection (AMR), which is strongly correlated with donor-specific anti-HLA antibodies (DSA), brings a poor outcome. Thus, to diagnose and treat AMR correctly is a clear proposition. In this review, we would like to focus on the detection of intra-graft DSA as a recent trend. Overall, here we will review the current knowledge regarding MHC, especially with intra-graft DSA, and future perspectives: HLA epitope matching; eplet risk stratification; predicted indirectly recognizable HLA epitopes etc. in the context of organ transplantation.

scholarly journals Flowering plant embryos: How did we end up here?

2021 ◽  
Author(s):  
Stefan A. Rensing ◽  
Dolf Weijers
Keyword(s):  
Current Knowledge ◽  
General Structure ◽  
Three Dimensional ◽  
Flowering Plants ◽  
Flowering Plant ◽  
Adult Plant ◽  
Ancestral State ◽  
Evolutionary Trajectory ◽  
Current State ◽  
Plant Embryo

AbstractThe seeds of flowering plants are sexually produced propagules that ensure dispersal and resilience of the next generation. Seeds harbor embryos, three dimensional structures that are often miniatures of the adult plant in terms of general structure and primordial organs. In addition, embryos contain the meristems that give rise to post-embryonically generated structures. However common, flowering plant embryos are an evolutionary derived state. Flowering plants are part of a much larger group of embryo-bearing plants, aptly termed Embryophyta. A key question is what evolutionary trajectory led to the emergence of flowering plant embryos. In this opinion, we deconstruct the flowering plant embryo and describe the current state of knowledge of embryos in other plant lineages. While we are far yet from understanding the ancestral state of plant embryogenesis, we argue what current knowledge may suggest and how the knowledge gaps may be closed.

scholarly journals Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Ce Yuan ◽  
Melanie Graham ◽  
Christopher Staley ◽  
Subbaya Subramanian
Keyword(s):  
Colorectal Cancer ◽  
Cardiovascular Disease ◽  
Nonhuman Primates ◽  
Current Knowledge ◽  
Distal Colon ◽  
Food Sources ◽  
Integrated Analysis ◽  
Strongly Correlated ◽  
Dietary Component ◽  
Metabolic Interactions

ABSTRACT The intestinal microbiota is highly metabolically active and plays an important role in many metabolic processes absent from the human host. Altered microbiota metabolism has been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. However, there is a gap in the current knowledge on how the microbiota interact with its host in terms of metabolic interactions. Here, we performed an integrated analysis between the mucosa-associated microbiota and the mucosa metabolome in healthy, nonhuman primates to investigate these relationships. The microbiota composition was distinct at each tissue location, with variation by host individual also observed. Microbiota-metabolome dynamics were primarily driven by interactions in the distal colon. These interactions were strongly correlated with dietary component, indicating a possibility to modulate microbiota-metabolomic interactions using prebiotic strategies. IMPORTANCE In a healthy colon, the microbiota produces a vast amount of metabolites that are essential to maintaining homeostasis in the colon microenvironment. In fact, these metabolites produced by the microbiota have been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. In this study, we used healthy nonhuman primate models to investigate the relationship between microbiota and tissue metabolites. We found that both microbiota and metabolites have location-specific signatures along the intestine. Most importantly, we found that metabolites from food sources correlate with multiple bacteria in different intestinal locations. Overall, this work presents a systems-level map of the association between the microbiota and the metabolites in healthy nonhuman primates, provides candidates for experimental validation, and suggests a possibility to regulate the gut microbiota through specific prebiotic combinations.

scholarly journals Molecular mechanisms mediating root hydrotropism: what we have observed since the rediscovery of hydrotropism

2019 ◽  
Vol 133 (1) ◽  
pp. 3-14
Author(s):  
Yutaka Miyazawa ◽  
Hideyuki Takahashi
Keyword(s):  
Arabidopsis Thaliana ◽  
Water Potential ◽  
Water Availability ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Potential Gradient ◽  
Regulatory Mechanisms ◽  
Directional Growth ◽  
Plant Adaptation ◽  
Water Potential Gradient

AbstractRoots display directional growth toward moisture in response to a water potential gradient. Root hydrotropism is thought to facilitate plant adaptation to continuously changing water availability. Hydrotropism has not been as extensively studied as gravitropism. However, comparisons of hydrotropic and gravitropic responses identified mechanisms that are unique to hydrotropism. Regulatory mechanisms underlying the hydrotropic response appear to differ among different species. We recently performed molecular and genetic analyses of root hydrotropism in Arabidopsis thaliana. In this review, we summarize the current knowledge of specific mechanisms mediating root hydrotropism in several plant species.

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