Development and characterization of 26 novel microsatellite loci for the trochid gastropodGibbula divaricata(Linnaeus, 1758), using IlluminaMiSeqnext generation sequencing technology

Using high-throughput sequencing technology 17 polymorphic microsatellites with perfect tetra-nucleotide repeats were identified for the brown spiny lobsterPanulirus echinatusSmith, 1869. Two to ten alleles were detected per locus across 30 samples analysed from the Canary Archipelago. Observed and expected heterozygosities per locus ranged between 0.100 and 0.867 and 0.095 and 0.799, respectively. No significant linkage disequilibrium was found between pairs of loci, and only one locus (Pe-L43) deviated from Hardy-Weinberg equilibrium, likely due to the presence of null alleles. Despite its economic importance and the threat of overfishing, population genetics studies of this species are lacking. Therefore, these 17 novel microsatellites markers will be a useful genetic resource for future conservation studies ofP. echinatus.

Download Full-text

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

10.7287/peerj.preprints.2559v1 ◽

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.

Download Full-text

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

10.7287/peerj.preprints.2559 ◽

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.

Download Full-text

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

Amphibia-Reptilia ◽

10.1163/15685381-00003030 ◽

2016 ◽

Vol 37 (1) ◽

pp. 121-125 ◽

Cited By ~ 1

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.

Download Full-text

Characterization of Novel Microsatellite Loci for Primula poissonii (Primulaceae) Using High-Throughput Sequencing Technology

Molecules ◽

10.3390/molecules21050536 ◽

2016 ◽

Vol 21 (5) ◽

pp. 536

Author(s):

Yun-Jiao Liu ◽

Cai-Yun Zhang ◽

Gang Hao ◽

Xue-Jun Ge ◽

Hai-Fei Yan

Keyword(s):

High Throughput ◽

Microsatellite Loci ◽

High Throughput Sequencing ◽

Sequencing Technology

Download Full-text

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

Amphibia-Reptilia ◽

10.1163/15685381-00003003 ◽

2015 ◽

Vol 36 (3) ◽

pp. 318-324 ◽

Cited By ~ 1

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.

Download Full-text

Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽

10.7717/peerj.2936 ◽

2017 ◽

Vol 5 ◽

pp. e2936 ◽

Cited By ~ 13

Author(s):

Caroline E. Dubé ◽

Serge Planes ◽

Yuxiang Zhou ◽

Véronique Berteaux-Lecellier ◽

Emilie Boissin

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Microsatellite Loci ◽

Natural Populations ◽

454 Sequencing ◽

Genetic Distances ◽

Null Alleles ◽

Future Research ◽

Significant Linkage ◽

Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Download Full-text

A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

Plant Genetic Resources ◽

10.1017/s1479262117000193 ◽

2017 ◽

Vol 16 (3) ◽

pp. 284-287

Author(s):

Bruno C. Rossini ◽

Mariá B. Kampa ◽

Celso L. Marino ◽

Fernanda Bortolanza Pereira ◽

Fábio M. Alves ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Loci ◽

Null Alleles ◽

Germplasm Resources ◽

Significant Linkage Disequilibrium ◽

Orchid Species ◽

Expected Heterozygosity ◽

Tropical Orchid ◽

Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

Download Full-text

Deviation from Hardy–Weinberg equilibrium, and temporal instability in allele frequencies at microsatellite loci in a local population of Atlantic cod

ICES Journal of Marine Science ◽

10.1016/j.icesjms.2005.05.009 ◽

2005 ◽

Vol 62 (8) ◽

pp. 1588-1596 ◽

Cited By ~ 25

Author(s):

Sten Karlsson ◽

Jarle Mork

Keyword(s):

Microsatellite Loci ◽

Atlantic Cod ◽

Local Population ◽

Allele Frequencies ◽

Null Alleles ◽

P Value ◽

Patchy Distribution ◽

Hardy Weinberg Equilibrium ◽

The One ◽

Weinberg Expectation

Abstract A total of 1455 spawning cod, sampled from a local spawning area in Trondheimsfjord (Norway) between 1985 and 2002, was screened at the microsatellite loci Gmo132 and Gmo2. Samples from 15 spawning years comprising 29 consecutive cohorts were analysed. At the Gmo132 locus, but not at Gmo2, allele frequencies varied significantly among sampling years as well as cohorts, corresponding to FST-values of 0.004 and 0.006, respectively. Both loci showed examples of significant deviations from Hardy–Weinberg expectation within sampling years as well as cohorts, manifested as deficiencies of heterozygotes. Combining the p-values from the single tests (Fisher's method) revealed an overall significant p-value for deviation from the Hardy–Weinberg expectations at Gmo132 but not at Gmo2. Trend tests showed significant HW deficiencies at both loci for annual samples but not for cohorts. Possible reasons for the deficiencies were discussed; inter alia the existence of null alleles, or a form of pseudo Wahlund effect due to a patchy distribution of habitats for settling O-group cod in the Trondheimsfjord. It was noted that there might be a relationship between the relatively high temporal within-population variability of allele frequencies at Gmo132 and the fact that among microsatellite loci studied so far, Gmo132 is the one that usually shows the highest genetic differentiation geographically in cod.

Download Full-text

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

10.20944/preprints201808.0409.v1 ◽

2018 ◽

Cited By ~ 1

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.

Download Full-text