scholarly journals Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis

2008 ◽  
Vol 2 ◽  
pp. BBI.S561 ◽  
Author(s):  
Zhenkang Xu ◽  
Laura Gutierrez ◽  
Matthew Hitchens ◽  
Steve Scherer ◽  
Amy K. Sater ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Microsatellite Loci ◽  
Bioinformatics Analysis ◽  
Pairwise Comparisons ◽  
Entire Genome ◽  
Microsatellite Repeats ◽  
Tropicalis Genome ◽  
Polymorphic Microsatellite ◽  
Tetranucleotide Microsatellites ◽  
Genomic Microsatellites

The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.

Isolation and characterisation of 12 polymorphic microsatellite loci for the threatened mound-building malleefowl, Leipoa ocellata (Aves : Megapodiidae)

2016 ◽  
Vol 64 (1) ◽  
pp. 33
Author(s):  
Taneal M. Cope ◽  
Terry Bertozzi ◽  
Raoul A. Mulder ◽  
Stephen C. Donnellan
Keyword(s):  
Microsatellite Loci ◽  
454 Pyrosequencing ◽  
Polymorphic Markers ◽  
Single Population ◽  
Microsatellite Repeats ◽  
The Family ◽  
Flanking Sequences ◽  
Polymorphic Microsatellite ◽  
Enrichment Techniques ◽  
Alectura Lathami

Using 454 pyrosequencing and genomic enrichment techniques we developed 12 polymorphic markers for the endangered megapode, the malleefowl (Leipoa ocellata). Pyrosequencing on a 454 instrument resulted in 65 536 reads, with 3469 containing microsatellite repeats. Of these, 232 contained unique flanking sequences and had more than 8 repeat motifs. We chose 13 loci based on reliability of amplification and, from these, 12 unlinked loci were selected for genotyping. In a single population (n = 19), the 12 markers were moderately polymorphic (number of alleles per locus range = 3–7) and showed moderate to high levels of heterozygosity (0.285–0.882). Nine microsatellite primer pairs developed from the brush turkey (Alectura lathami), the closest living relative of the malleefowl in the family, Megapodiidae, failed to reliably amplify malleefowl DNA.

Genetic Diversity and Structure of the Nile Soft-Shelled Turtle (Trionyx triunguis) Along the Mediterranean coast of Turkey

2020 ◽  
Vol 27 (6) ◽  
pp. 307-315
Author(s):  
Özgür Güçlü ◽  
Bülent Bozdoğan
Keyword(s):  
Microsatellite Loci ◽  
Geographic Distance ◽  
Iucn Red List ◽  
Genetic Variations ◽  
Mediterranean Coast ◽  
Critically Endangered ◽  
Mediterranean Populations ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
The Mediterranean

The Nile soft-shelled turtle (Trionyx triunguis) is distributed between Dalyan and Samandağ throughout the Mediterranean coast in Turkey. The Mediterranean subpopulation of the Nile soft-shelled turtle is listed as critically endangered in the IUCN Red List Categories. This investigation aimed to determinate levels of genetic variations and patterns of genetic structures among Mediterranean populations in Turkey by using T. triunguis-specific microsatellite primers. A total of 13 polymorphic microsatellite loci were studied among samples of 121 individuals collected from five populations in Turkey. Of 13 polymorphic microsatellite loci used, 3 new were identified in this study. The genetic differentiation among the 5 studied populations of T. triunguis was significant (p 0.001). The analysis of molecular variance (AMOVA) indicated that genetic variations occurred mainly within populations (89.7%) rather than among populations (10.3%). Structure analysis showed presence of two main groups among the Mediterranean T. triunguis populations. However genetic variations among populations were not correlated with geographic distance between the locations. Analysis of data showed that one of the populations (Dalyan) had undergone a bottleneck effect. Migration analysis indicates that T. triunguis migrates between five Mediterranean populations in Turkey. We concluded that based on our results the status of ‘critically endangered’ of T. triunguis should be maintained. Long term population genetic survey studies should be undertaken and changes in habitats of T. triunguis populations, as well as their population size and structure should be monitored for each population to be able to establish a clear strategy for protection of T. triunguis.

scholarly journals Stand out from the Crowd: Small-Scale Genetic Structuring in the Endemic Sicilian Pond Turtle

Diversity ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 343
Author(s):  
Luca Vecchioni ◽  
Federico Marrone ◽  
Marco Arculeo ◽  
Uwe Fritz ◽  
Melita Vamberger
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Small Scale ◽  
Moderate Degree ◽  
Geographical Pattern ◽  
Genetic Structuring ◽  
Pond Turtle ◽  
Emys Trinacris ◽  
Polymorphic Microsatellite ◽  
Entire Distribution

The geographical pattern of genetic diversity was investigated in the endemic Sicilian pond turtle Emys trinacris across its entire distribution range, using 16 microsatellite loci. Overall, 245 specimens of E. trinacris were studied, showing high polymorphic microsatellite loci, with allele numbers ranging from 7 to 30. STRUCTURE and GENELAND analyses showed a noteworthy, geographically based structuring of the studied populations in five well-characterized clusters, supported by a moderate degree of genetic diversity (FST values between 0.075 and 0.160). Possible explanations for the genetic fragmentation observed are provided, where both natural and human-mediated habitat fragmentation of the Sicilian wetlands played a major role in this process. Finally, some conservation and management suggestions aimed at preventing the loss of genetic variability of the species are briefly reported, stressing the importance of considering the five detected clusters as independent Management Units.

Polymorphic microsatellite loci from the West Nile virus vector Culex tarsalis

2006 ◽  
Vol 6 (3) ◽  
pp. 680-682 ◽  
Author(s):  
JASON L. RASGON ◽  
MEERA VENKATESAN ◽  
CATHERINE J. WESTBROOK ◽  
MARY CLAIRE HAUER
Keyword(s):  
West Nile Virus ◽  
Microsatellite Loci ◽  
Virus Vector ◽  
Culex Tarsalis ◽  
The West ◽  
West Nile ◽  
Polymorphic Microsatellite

Isolation and characterization of fourteen polymorphic microsatellite loci for Odontobutis sinensis

2014 ◽  
Vol 6 (3) ◽  
pp. 711-713
Author(s):  
Ping Qiu ◽  
Xuefen Yang ◽  
Kai-Jian Wei ◽  
Zhihong Ma ◽  
Ruibin Yang
Keyword(s):  
Microsatellite Loci ◽  
Isolation And Characterization ◽  
Polymorphic Microsatellite

Development of nineteen novel polymorphic microsatellite loci of Clupeichthys aesarnensis

2013 ◽  
Vol 5 (3) ◽  
pp. 707-709
Author(s):  
Noriyuki Koizumi ◽  
Shinsuke Morioka ◽  
Atsushi Mori ◽  
Bounsong Vongvichith ◽  
Koichi Shibukawa ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Polymorphic Microsatellite
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