Development and characterization of new polymorphic microsatellite loci for Trionyx triunguis (Testudines: Trionychidae) in the Mediterranean Basin

2015 ◽  
Vol 36 (3) ◽  
pp. 318-324 ◽  
Author(s):  
Özgür Güçlü ◽  
Salih Hakan Durmuş ◽  
Kamil Candan ◽  
Nurettin Beşer ◽  
Süheyla Türkyilmaz ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Captive Breeding ◽  
Null Alleles ◽  
Enriched Library ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
The Mediterranean ◽  
Captive Breeding Programs

The Mediterranean subpopulation of T. triunguis has been listed by IUCN as critically endangered (European Reptile and Amphibian Specialist Group 1996, category CR C2A). There are very few studies for determination of distribution and population genetics of this species in the world. A total of 13 polymorphic microsatellite loci were isolated from 42 samples of T. triunguis by using biotinylated (GT)10, (CT)10, (GATA)5-enriched library. The range of observed heterozygosities was 0.000-0.833 with a mean of 0.274, and the range of expected heterozygosities was 0.081-0.607 with a mean of 0.374. It was found that four loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni correction analysis. There was no evidence for large allele dropout. Null alleles may be present at ttmed-6, ttmed-8, and ttmed-9 loci, as suggested by the general excess of homozygote for most allele size classes. Designed microsatellite loci could provide a powerful tool for the population structure and conservation genetics studies of the Nile soft-shelled turtle and for captive breeding programs or to detect species illegal trade.

Characterization of 17 novel microsatellite loci in the Nile monitor (Varanus niloticus) via 454 pyrosequencing

2016 ◽  
Vol 37 (1) ◽  
pp. 121-125 ◽  
Author(s):  
Jared P. Wood ◽  
Todd S. Campbell ◽  
Robert B. Page
Keyword(s):  
Microsatellite Loci ◽  
454 Pyrosequencing ◽  
Sequence Similarity ◽  
Null Alleles ◽  
The Us ◽  
Hardy Weinberg Equilibrium ◽  
The City ◽  
Two Populations ◽  
Genotypic Disequilibrium

We used 454 pyrosequencing to characterize 17 novel microsatellite loci from the Nile monitor (Varanus niloticus), using samples from an invasive population in the US state of Florida. These markers were screened for variation in 40 individuals from the City of Cape Coral. Observed heterozygosity ranged from 0.18 to 0.73 (mean ± SE = 0.46 ± 0.06) and the number of alleles per locus ranged from 1 to 4 (mean ± SE = 2.5 ± 0.2). Preliminary genotyping of samples from populations in West Palm Beach and Homestead revealed two loci (Mon6andMon15) that are monomorphic in Cape Coral, but polymorphic in these other two populations. We found no statistical departures from Hardy-Weinberg equilibrium or evidence of null alleles. However, there was statistical evidence for genotypic disequilibrium betweenMon1-Mon14andMon3-Mon8. BLASTn searches of NCBI’s nr/nt database identified four microsatellites containing 454 fragments that exhibit substantial sequence similarity to loci in other reptilian genomes, suggesting these markers should be prioritized by researchers interested in cross-amplification in other varanids. The resources we have developed will enable investigations of the population genetic dynamics of invasive Nile monitors in Florida and may facilitate studies within this species native range.

scholarly journals Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

2016 ◽  
Author(s):  
Nathan K Truelove ◽  
Loong Fai Ho ◽  
Richard F Preziosi ◽  
Stephen J. Box
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Null Allele ◽  
Florida Keys ◽  
Illumina Miseq ◽  
Allele Frequencies ◽  
Null Alleles ◽  
Queen Conch ◽  
Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

scholarly journals Isolation and Characterization of Polymorphic Microsatellite loci from the Invasive Worm Branchiomma luctuosum (Grube, 1870) (Annelida: Sabellidae)

2018 ◽  
Author(s):  
Flávia Ariany Belato ◽  
Elisa Maria Costa-Paiva ◽  
Paulo Cesar Paiva ◽  
Anderson Vilasboa
Keyword(s):  
Null Alleles ◽  
Anthropogenic Activity ◽  
Brazilian Coast ◽  
Isolation And Characterization ◽  
History Of ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
High Level ◽  
Activity Areas

Introduction of exotic species in new areas through anthropic action is one of the major problems that can affect biodiversity. Branchiomma luctuosum is known for its highly invasive potential and the actual occurrence of species commonly associated with port activity areas is an extra evidence that this anthropogenic activity should not be underestimated. In order to develop suitable molecular markers for future studies on colonization routes and population dynamics of the invading individuals of B. luctuosum, nine highly polymorphic microsatellite loci were isolated and their polymorphism levels were evaluated. These loci showed a range of number of alleles per locus from five to ten and all loci had a high level of genetic diversity, and exhibited significant heterozygote deficiencies probably due to the presence of null alleles. Significant deviations from the Hardy-Weinberg equilibrium were detected at several loci and most of them were related to a heterozygous deficit. Heterozygous deficiency can be expected in this case due to the biology and history of this invasive species, in relation to its recent introduction in Brazilian coast and possible action of multiple introductory events.

scholarly journals Isolation and Characterization of Polymorphic Microsatellite loci from the Invasive Worm Branchiomma luctuosum (Grube, 1870) (Annelida: Sabellidae)

2018 ◽  
Author(s):  
Flávia Ariany Belato ◽  
Elisa Costa-Paiva ◽  
Anderson Vilasboa
Keyword(s):  
Null Alleles ◽  
Anthropogenic Activity ◽  
Brazilian Coast ◽  
Isolation And Characterization ◽  
History Of ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
High Level ◽  
Activity Areas

Introduction of exotic species in new areas through anthropic action is one of the major problems that can affect biodiversity. Branchiomma luctuosum is known for its highly invasive potential and the actual occurrence of species commonly associated with port activity areas is an extra evidence that this anthropogenic activity should not be underestimated. In order to develop suitable molecular markers for future studies on colonization routes and population dynamics of the invading individuals of B. luctuosum, nine highly polymorphic microsatellite loci were isolated and their polymorphism levels were evaluated. These loci showed a range of number of alleles per locus from five to ten and all loci had a high level of genetic diversity, and exhibited significant heterozygote deficiencies probably due to the presence of null alleles. Significant deviations from the Hardy-Weinberg equilibrium were detected at several loci and most of them were related to a heterozygous deficit. Heterozygous deficiency can be expected in this case due to the biology and history of this invasive species, in relation to its recent introduction in Brazilian coast and possible action of multiple introductory events.

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.

New Microsatellite Markers for Two Sympatric Tinamou Species, the Ornate Tinamou (Nothoprocta ornata) and Darwin's Nothura (Nothura darwinii)

2016 ◽  
Vol 9 (3) ◽  
pp. 139-146 ◽  
Author(s):  
Lina Maria Giraldo Deck ◽  
Jan Christian Habel ◽  
Manuel Curto ◽  
Martin Husemann ◽  
Sarah Sturm ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Life History Traits ◽  
Null Alleles ◽  
Genetic Population ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Successful Amplification ◽  
Low Coverage ◽  
Candidate Loci

Tinamous (Tinamidae) represent one of the most ancient living avian lineages but their life history traits are relatively unstudied. Here we identified microsatellite loci for two sympatric tinamou species, the Ornate Tinamou ( Nothoprocta ornata) and the Darwin's Nothura ( Nothura darwinii) from low coverage Illumina sequencing of genomic DNA. The experiment yielded a large number of candidate loci. We designed primers and tested them for successful amplification in 1 to 2 populations of the target species, tested for deviation from the Hardy–Weinberg equilibrium and the presence of null alleles, the levels of polymorphism and potential cross-amplification. All 30 and 24 loci amplified consistently, in the Ornate Tinamou and in Darwin's Nothura, respectively. In the Ornate Tinamou, 25 loci were polymorphic and in the Darwin's Nothura 12, with 2 to 14 alleles per locus in both species. The expected heterozygosity ranged from 0.054 to 0.917 in the Ornate Tinamou and from 0.044 to 0.908 in the Darwin's Nothura. 23 (40%) of 54 loci were successfully cross-amplified. These newly discovered, polymorphic microsatellite loci represent a valuable tool for future studies on social behaviour, parentage and genetic population structure in tinamous.

scholarly journals Isolation and Characterization of Polymorphic Microsatellite Markers for Two Subterranean Termites

Sociobiology ◽  
2017 ◽  
Vol 64 (3) ◽  
pp. 352 ◽  
Author(s):  
Yu-Lei Dang ◽  
Hong-Gui Zhang ◽  
Yu-Feng Meng ◽  
Min Zhang ◽  
Sha Zhao ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
Subterranean Termites ◽  
Polymorphic Markers ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite

We isolated 15 and 18 highly polymorphic genomic microsatellite markers from two subterranean termites, Reticulitermes aculabialis and R. labralis, respectively. A total of 53 alleles were detected in 15 microsatellite loci of R. aculabialis, and the alleles were 3.533±1.302 (mean±SD), while the corresponding data of R. labralis were 115 detected alleles in 18 microsatellite loci with 6.389±1.754 alleles. The observed and expected heterozygosity was 0.496±0.236 and 0.564±0.125 in R. aculabialis, and 0.368±0.263 and 0.702±0.115 in R. labralis, respectively. Seven loci were highly polymorphic (PIC>0.5) in R. aculabialis, and 15 loci were highly polymorphic (PIC>0.5) in R. labralis. All loci showed Hardy–Weinberg equilibrium. These polymorphic markers provide useful tools for population genetic and breeding system studies of subterranean termites.

scholarly journals Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

2016 ◽  
Author(s):  
Nathan K Truelove ◽  
Loong Fai Ho ◽  
Richard F Preziosi ◽  
Stephen J. Box
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Null Allele ◽  
Florida Keys ◽  
Illumina Miseq ◽  
Allele Frequencies ◽  
Null Alleles ◽  
Queen Conch ◽  
Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

Characterization of new polymorphic microsatellite loci for the lesser tree frog (Dendropsophus minutus)

2015 ◽  
Vol 36 (1) ◽  
pp. 83-86
Author(s):  
Hilton M. Oyamaguchi ◽  
Hilton M. Oyamaguchi ◽  
Ryo P. Okubo ◽  
Hilton M. Oyamaguchi ◽  
Ryo P. Okubo ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Taxonomic Status ◽  
Tree Frog ◽  
Expected Heterozygosity ◽  
Scale Population ◽  
Hardy Weinberg Equilibrium ◽  
Taxonomic Confusion ◽  
Polymorphic Microsatellite ◽  
Roche 454

Dendropsophus minutus is a widely distributed species in South America and presents great phenotypic variation which has led to taxonomic confusion. Herein we describe nine microsatellite loci for D. minutus discovered by genomic shotgun sequencing using Roche 454 pyrosequencing. These microsatellite loci were tested on a panel of 29 individuals. All nine loci were polymorphic (11-22 alleles) with observed heterozygosity ranging from 0.42 to 0.90 and expected heterozygosity from 0.75 to 0.94. Three loci deviated from the Hardy-Weinberg equilibrium. These characterized polymorphic markers for D. minutus will enable investigation of fine scale population structure, evolutionary processes, and clarify taxonomic status. This genetic information will be useful in conservation decisions regarding on this apparently wide distributed species.

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