scholarly journals Transcriptome-Derived Microsatellite Markers for Population Diversity Analysis in Archidendron Clypearia (Jack) I.C. Nielsen

2021 ◽  
Author(s):  
Dandan Li ◽  
Mei Li ◽  
Fagen Li ◽  
Qijie Weng ◽  
Changpin Zhou ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
De Novo ◽  
Population Diversity ◽  
Diversity Analysis ◽  
Flower Bud ◽  
High Genetic Diversity ◽  
Genetic Studies ◽  
Practical Applications ◽  
Two Populations

Abstract Genomic resources including transcriptomic sequences and molecular markers remain scarce in the medicinally important woody legume genus Archidendron F. Mueller. Here we conducted transcriptome sequencing, genic microsatellite marker development, and population diversity analysis in Archidendron clypearia (Jack) I.C. Nielsen. Flower and flower bud transcriptomes were de novo assembled into 173,172 transcripts, with an average transcript length of 1597.3 bp and an N50 length of 2427 bp. A total of 34,701 microsatellite loci were identified from 26,716 (15.4%) transcripts. Primer pairs were designed for 718 microsatellite loci, of which 456 (63.5%) were polymorphic. Of the 456 polymorphic markers, 391 (85.7%) and 402 (88.1%) were transferable to A. lucidum (Benth.) I.C. Nielsen and A. multifoliolatum (H.Q. Wen) T.L. Wu, respectively. Using a subset of 15 microsatellite markers, relatively high genetic diversity was detected over two A. clypearia populations, with overall mean expected heterozygosity (He) being 0.707 and demonstrating the necessity of conservation. Relatively low differentiation between the two populations was revealed despite the distant separation (about 700 km), with overall inbreeding coefficient of sub-population to the total population (Fst) being 8.7%. This suggests that A. clypearia has mainly an outcrossing mating system and weak genetic structure. These results will offer valuable resources and information for further genetic studies and practical applications in Archidendron and the related taxa.

scholarly journals De novo developed microsatellite markers in gill parasites of the genus Dactylogyrus (Monogenea): revealing the phylogeographic pattern of population structure in the generalist parasite Dactylogyrus vistulae

2021 ◽  
Author(s):  
Michal Benovics ◽  
Lenka Gettová ◽  
Andrea Simková
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Parasite Species ◽  
De Novo ◽  
High Genetic Diversity ◽  
Genetic Studies ◽  
The North ◽  
Gill Parasites ◽  
Modern Population

Approaches using microsatellite markers are considered the gold standard for modern population-genetic studies. However, though they have found application in research into various platyhelminth taxa, they remained substantially underutilized in the study of monogeneans. In the present study, a newly-developed set of 24 microsatellite markers was used to investigate the genetic diversity of the generalist monogenean species D. vistulae. The analyzed parasite specimens were collected from 13 cyprinoid species from 11 sites in the Apennine and Balkan peninsulas. A total of 159 specimens were genotyped at each of the loci and the number of alleles per locus ranged from 2 to 16, with a mean number of 6.958 alleles per locus. Exceptionally high genetic diversity was observed among D. vistulae individuals in the southern Balkans, suggesting that this region might represent the center of diversification of the genus in Europe, from where Dactylogyrus parasites expanded into the north. The initial clustering analysis divided all investigated specimens into three major clusters; however, the results of the subsequent analyses revealed the existence of various subpopulations, suggesting that the population structure of D. vistulae is associated with the diversification of their cyprinoid hosts. In addition, partition of the parasite population was observed in regions of the sympatric occurrence of two host species, indicating that these hosts may represent a barrier to gene flow, even for generalist parasite species.

scholarly journals Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacleChelonibia testudinaria(Linnaeus, 1758)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2019 ◽  
Author(s):  
Christine Ewers-Saucedo ◽  
John D. Zardus ◽  
John P. Wares
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Next Generation Sequencing Data ◽  
Model Organisms ◽  
Next Generation ◽  
Sequencing Data ◽  
Genetic Studies ◽  
Evolutionary Features ◽  
Generation Sequencing

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacleChelonibia testudinaria(Linnaeus, 1758).Chelonibia testudinariaappears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies onC. testudinaria.

scholarly journals Isolation and Characterization of Twenty Polymorphic Microsatellite Loci for Moringa oleifera (Moringaceae)

HortScience ◽  
2010 ◽  
Vol 45 (4) ◽  
pp. 690-692 ◽  
Author(s):  
Jiang-Chong Wu ◽  
Jing Yang ◽  
Zhi-Jian Gu ◽  
Yan-Ping Zhang
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
Moringa Oleifera ◽  
Microsatellite Primers ◽  
Genetic Studies ◽  
Isolation And Characterization ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite

By using a modified biotin-streptavidin capturing method, a total of 20 polymorphic microsatellite markers were developed from Moringa oleifera Lam. (Moringaceae), a useful multipurpose tree. Twenty-four domesticated individuals, with germplasms of India and Myanmar, were used to screen polymorphism of these 20 microsatellite markers. The number of alleles per locus ranged from two to six. The expected and observed heterozygosity varied from 0.3608 to 0.7606 and from 0.0000 to 0.8750, respectively. Seven loci were significantly deviated from Hardy-Weinberg equilibrium. The availability of these microsatellite primers would provide a powerful tool for aspects of detailed population genetic studies of M. oleifera.

scholarly journals Short Note: Cross-Species Amplification and Characterization of Pinus Chloroplast Microsatellite Markers in Cedrus deodara Roxb.

2011 ◽  
Vol 60 (1-6) ◽  
pp. 65-69 ◽  
Author(s):  
H. S. Ginwal ◽  
P. Chauhan ◽  
S. Barthwal ◽  
A. Sharma ◽  
R. Sharma
Keyword(s):  
Microsatellite Markers ◽  
Short Note ◽  
Haplotype Diversity ◽  
Natural Populations ◽  
Chloroplast Microsatellite ◽  
Cedrus Deodara ◽  
Genetic Studies ◽  
Adult Trees ◽  
Two Populations

AbstractThe study reports the transferability of chloroplast microsatellite markers developed forPinusspecies toCedrus deodara. A total of 49 primer pairs (both nuclear and chloroplast) of Pinus species were tested inC. deodaraout of which 21 chloroplast primers showed positive amplification and 20 were found polymorphic. The primers were screened on 100 adult trees of two natural populations ofC. deodara. Using twenty cpSSR primers, a total of 64 variants were found which combined in 70 different haplotypes. The total haplotype diversity in two populations was 0.860 and 0.876 with a mean of 0.868. These sets of markers can further be used for population genetic studies and characterization inC. deodarafor which no cpSSR markers have been reported till date.

scholarly journals Genetic diversity and structure of Chinese grass shrimp, Palaemonetes sinensis, inferred from transcriptome-derived microsatellite markers

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yingying Zhao ◽  
Xiaochen Zhu ◽  
Zhi Li ◽  
Weibin Xu ◽  
Jing Dong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
In Situ Conservation ◽  
Grass Shrimp ◽  
The Other ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
Two Populations

Abstract Background The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome. Results Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (FST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis. Conclusion This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.

Cross-species amplification from crop soybean Glycine max provides informative microsatellite markers for the study of inbreeding wild relatives

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 382-393 ◽  
Author(s):  
K Hempel ◽  
R Peakall
Keyword(s):  
Glycine Max ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Related Species ◽  
De Novo ◽  
Wild Relatives ◽  
Population Mean ◽  
Size Homoplasy ◽  
Effective Use ◽  
Polymorphism Level

The development of microsatellite markers through transfer of primers from related species (cross-species amplification) remains a little-explored alternative to the de novo method in plants. In this study of 100 microsatellite loci from Glycine max, we examined two aspects of primer transfer. First, we tested if source locus properties can predict primer transfer and polymorphism in Glycine cyrtoloba and Glycine clandestina. We transferred 23 primers to G. cyrtoloba and 42 to G. clandestina, with 19 loci polymorphic within G. clandestina. However, we could not predict transfer or polymorphism from the source locus properties. Second, we evaluated the subset of 11 polymorphic loci for study in G. clandestina populations representing two local morphotypes. All loci were informative within populations (population mean He ± SE = 0.58 ± 0.04). We directly sequenced 28 alleles at 4 representative loci. The allelic patterns and sequencing results established that 8 of 11 loci were typical microsatellites, confirming the utility of primer transfer as an alternative to de novo development. Additionally, we found that morphotypic differentiation between populations was paralleled by changes in polymorphism level at six loci and size homoplasy at one locus. We interpret these patterns as being a product of selfing in G. clandestina. Our results demonstrate the value of allele sequence knowledge for the most effective use of microsatellites.Key words: microsatellite transfer predictability, cross-species amplification, Glycine, selfing, size homoplasy.

scholarly journals Construction of Microsatellite Linkage Maps for Corymbia

2006 ◽  
Vol 55 (1-6) ◽  
pp. 228-238 ◽  
Author(s):  
M. Shepherd ◽  
S. Kasem ◽  
D. Lee ◽  
R. Henry
Keyword(s):  
Comparative Analysis ◽  
Microsatellite Markers ◽  
De Novo ◽  
Convincing Evidence ◽  
Linkage Groups ◽  
Single Linkage ◽  
Hybrid Inviability ◽  
Genetic Studies ◽  
Tropical Forestry ◽  
Close Relationship

Abstract The genus Corymbia is closely related to the genus Eucalyptus, and like Eucalyptus contains tree species that are important for sub-tropical forestry. Corymbia’s close relationship with Eucalyptus suggests genetic studies in Corymbia should benefit from transfer of genetic information from its more intensively studied relatives. Here we report a genetic map for Corymbia spp. based on microsatellite markers identified de novo in Corymbia sp or transferred from Eucalyptus. A framework consensus map was generated from an outbred F2 population (n = 90) created by crossing two unrelated Corymbia torelliana × C. citriodora subsp. variegata F1 trees. The map had a total length of 367 cM (Kosambi) and was composed of 46 microsatellite markers distributed across 13 linkage groups (LOD 3). A high proportion of Eucalyptus microsatellites (90%) transferred to Corymbia. Comparative analysis between the Corymbia map and a published Eucalyptus map identified eight homeologous linkage groups in Corymbia with 13 markers mapping on one or both maps. Further comparative analysis was limited by low power to detect linkage due to low genome coverage in Corymbia, however, there was no convincing evidence for chromosomal structural differences because instances of non-synteny were associated with large distances on the Eucalyptus map. Segregation distortion was primarily restricted to a single linkage group and due to a deficit of hybrid genotypes, suggesting that hybrid inviability was one factor shaping the genetic composition of the F2 population in this inter-subgeneric hybrid. The conservation of microsatellite loci and synteny between Corymbia and Eucalyptus suggests there will be substantial value in exchanging information between the two groups.

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

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