Fifteen polymorphic microsatellite markers for the giant spiny frog, Paa spinosa

We characterized 15 polymorphic microsatellite loci for the giant spiny frog, Paa spinosa. These loci were highly polymorphic when screened in 38 individuals from two different populations, with nine to 23 alleles per locus. The range of observed and expected heterozygosities was 0.231-0.916 and 0.296-0.944, respectively. These polymorphic loci will be useful for assessing genetic diversity, population structure, gene flow, population assignment and determining paternity in the giant spiny frog.     

Ten polymorphic microsatellite DNA markers for the platypus, Ornithorhynchus anatinus

We identified and optimized 10 microsatellite loci for the platypus, Ornithorhynchus anatinus (Monotremata: Ornithorhynchidae), and screened 21 individuals from the southern tablelands area of New South Wales, Australia. Each polymorphic locus possessed between two and 12 alleles with observed heterozygosities between 0.118 and 0.950. The intent of this effort was to provide informative loci for studies on the population genetics of this species.     

Isolation and characterization of 19 polymorphic microsatellite DNA markers in the Japanese brown frog (Rana japonica)

We report the isolation and characterization of 19 polymorphic microsatellite DNA markers in the Japanese brown frog (Rana japonica). These markers were tested in 24 individuals each collected from three distinct populations in Ichikai-machi, Tochigi Prefecture. The number of observed alleles per locus ranged from 3 to 24 across all populations, and the values of observed and expected heterozygosities ranged from 0.130 to 1 and from 0.125 to 0.941, respectively. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species.     

Characterization of microsatellite loci for a barrenwort species (Epimedium diphyllum,Berberidaceae)

Microsatellites were identified and characterized from Epimedium diphyllum, a species of barrenworts, both attractive garden plants and valuable medicinal plants. Some Japanese species of Epimedium are threatened with extinction, and are listed in the Red Data Book of plants in Japan. Natural hybrid zones also have been reported among some taxa of Japanese Epimedium. We developed eight polymorphic microsatellite primers for population genetic analyses of E. diphyllum. The numbers of alleles per locus ranged from 10 to 20, with observed levels of heterozygosity between 0.85 and 1.00. These primer sets yielded amplification in the other three Japanese Epimedium. These markers will be valuable for conservation genetics, evolutionary biology, pharmacognostic study, and horticultural study of Epimedium.     

Development of 10 polymorphic microsatellite markers from herbicide‐bleached tissues of the brooding pocilloporid coral Seriatopora hystrix

Here we report the isolation of 44 microsatellites from the brooding, pocilloporid coral, Seriatopora hystrix, developed from a partial genomic DNA library using a repeat enrichment protocol. A further eight previously published microsatellites were also tested; five of these were developed for S. hystrix, whereas three were isolated from corals of the closely related genus Pocillopora. Out of these, we incorporated nine and 10 primer pairs into two multiplex reactions that reliably amplified polymorphic microsatellites in populations from the west and the east coast of Australia, respectively. Number of alleles ranged from three to 22 per locus.     

Characterization of polymorphic microsatellite markers for a coniferous shrub Juniperus sabina (Cupressaceae)

Juniperus sabina L. is an evergreen coniferous shrub, with a widespread distribution in Asia and Europe. It is one of the key species for restoration of the ecosystem in desertification areas. In the present study, we isolated and characterized eight microsatellite loci of this species. The number of alleles per locus ranged from two to 27, with observed heterozygosity values ranging from 0.256 to 0.744 and expected heterozygosity from 0.276 to 0.939. The markers developed in this study could be useful for population genetics studies of J. sabina.     

Characterisation of the complete mitochondrial genome and 13 microsatellite loci through next-generation sequencing for the New Caledonian spider-ant Leptomyrmex pallens

The complete mitochondrial genome and a set of polymorphic microsatellite markers were identified by 454 pyrosequencing (1/16th of a plate) for the New Caledonian rainforest spider-ant Leptomyrmex pallens. De novo genome assembly recovered the entire mitochondrial genome with mean coverage of 8.9-fold (range 1–27). The mitogenome consists of 15,591 base pairs including 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The genome arrangement is typical of insect taxa and very similar to the only other published ant mitogenome from the Solenopsis genus, with the main differences consisting of translocations and inversions of tRNAs. A total of 13 polymorphic loci were also characterized using 41 individuals from a single population in the Aoupinié region, corresponding to workers from 21 nests and 16 foraging workers. We observed moderate genetic variation across most loci (mean number of alleles per locus = 4.50; mean expected heterozygosity = 0.53) with evidence of only two loci deviating significantly from Hardy–Weinberg equilibrium due to null alleles. Marker independence was confirmed with tests for linkage disequilibrium. Most loci cross amplified for three additional Leptomyrmex species. The annotation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the colony structure, population genetic patterns, and dispersal strategy of L. pallens in the context of rainforest fragmentation in New Caledonia. Furthermore, this paper confirms a recent line of evidence that comprehensive mitochondrial data can be obtained relatively easily from small next-generation sequencing analyses. Greater synthesis of next-generation sequencing data will play a significant role in expanding the taxonomic representation of mitochondrial genome sequences.     

Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae)

We developed five highly polymorphic dinucleotide microsatellite loci for the grassland species Hypochaeris radicata (Asteraceae). Polymorphism of these markers was examined in six populations in the Netherlands. All loci were polymorphic in all populations. The number of alleles per locus varied between 18 and 43. Expected heterozygosity was between 0.86 and 0.91. Cross‐species amplification was tested in six Hypochaeris species and was successful for three different loci in four species. These microsatellites are a useful tool in population genetic, dispersal and metapopulation studies or in testing levels of inbreeding.     

Isolation and characterization of microsatellite markers from the hosta species Hosta albomarginata (Liliaceae)

Hostas are very popular ornamental plants in gardens in the United States, Europe, and East Asia. We have developed nine microsatellite loci from an enrichment library of genomic DNA in Hosta albomarginata. We characterized these nine microsatellite loci for 20 individuals from a population of H. albomarginata. The primers developed in this study yielded an average of 12.4 alleles per locus (range five to 20) and an average expected heterozygosity of 0.86 (range 0.65 to 0.95). These markers will be powerful tools for breeding programmes of hosta cultivars, studies of population genetics, and the conservation of wild hosta species.     

Characterization of polymorphic microsatellite loci in the aphid species Macrosiphum euphorbiae (Hemiptera: Aphididae)

Fourteen microsatellite loci were isolated and characterized in the potato aphid, Macrosiphum euphorbiae Thomas, by screening a genomic library with the oligonucleotide probes (GA)₁₀ (GT)₁₀ and (GATA)₄. Allelic diversity was estimated in samples collected from potato fields in Tunisia. Ten loci displayed polymorphism that ranged from two to four alleles per locus and the observed heterozygosity ranged from zero to one. These markers could be used to study the population genetic structure of this polyphagous aphid species.     

New polymorphic microsatellite loci for the Macedonian crested newt, Triturus macedonicus, and cross-priming testing in four other crested newt species

Eleven microsatellites have been characterized for Triturus macedonicus. Nine loci showed different variation patterns in a sample of 40 individuals from a single breeding pond in Zagori province (Greece), with an average number of 4.2 alleles per locus and an expected heterozygosity ranging from 0.1199 to 0.8079. Distinct cross-priming amplification rates were recovered on four additional crested newt species. Two monomorphic T. macedonicus loci were polymorphic in other Triturus species. The microsatellites developed herein could be a useful intraspecific genetic tool to undertake fine-scale population genetic analyses as well as in the study of contact zones between crested newt species.     

New polymorphic microsatellite loci for the Greek smooth newt, Lissotriton vulgaris graecus, and their utility in the nominotypical subspecies

Eight polymorphic microsatellites were isolated from the Greek smooth newt (Lissotriton vulgaris graecus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)(11) probe. The loci showed different variation patterns in a single breeding population (32 individuals) with mean number of alleles at 5.0 and mean observed heterozygosity at 0.520. The amplification success also in the nominotypical subspecies favours the use of these microsatellite loci in population genetic analyses as well as in the study of contact zones between smooth newt subspecies.     

Characterization of microsatellite markers for the endemic sand dune lizard,Sceloporus arenicolus

Here we characterize and report on the genetic variability of eight microsatellite loci for the endemic sand dune lizard, Sceloporus arenicolus, that amplified consistently for individuals throughout the species’ range. The number of alleles per locus was high (mean = 13.25) and observed heterozygosities ranged from 0.354 to 0.808. With the exception of a single locus, the loci did not deviate from Hardy–Weinberg expectations. This set of markers is currently being used to examine population structure and landscape genetics in S. arenicolus, a habitat specialist with a restricted range and patchy distribution.     

Characterization of polymorphic microsatellite markers for the blowfly Chrysomya albiceps (Diptera: Calliphoridae)

Chrysomya albiceps is a blowfly of great medical, sanitary and forensic importance widely distributed in the Afrotropical, southern Palaearctic, northern Oriental regions and, recently, in Central and South Americas. Here, we report the characterization of 13 polymorphic microsatellite markers for C. albiceps. The number of alleles ranged from three to 13 alleles with expected heterozygosities ranging from 0.4668 to 0.8408. These markers will be extremely useful for investigating many important aspects of this species such as population structure, dispersal and colonization dynamics.     

Development and characterization of eight polymorphic microsatellite markers for Daphnia atkinsoni (Crustacea: Ctenodaphnia)

A microsatellite‐enriched genomic library was developed for the water flea Daphnia atkinsoni Baird, 1859, a dominant species of intermittent wetlands in Europe. Eight polymorphic microsatellite markers were successfully optimized. Characterization of 77 individuals from Belgium and Spain showed moderate (in the former) to high (in the latter) levels of polymorphism with two to 11 alleles per locus and an observed heterozygosity ranging from 0 to 0.87. Some of these microsatellite markers were successfully amplified in three other Daphnia species (D. magna n = 4, D. similis n = 6; D. obtusa n = 6).     

Isolation and characterization of fourteen polymorphic microsatellite markers in the viperine snake Natrix maura

Nineteen polymorphic microsatellite loci were identified and developed for Natrix maura. Polymorphism was assessed for 120 individuals sampled across four sampling sites from the French Pyrenees Mountains. The number of alleles per locus ranged from 3 to 15, and expected heterozygosity per locus ranged from 0.227 to 0.863. We tested for deviation from Hardy–Weinberg equilibrium and linkage disequilibrium and assessed the presence of null alleles for all loci, resulting in a selection of 14 high‐quality polymorphic markers. These markers will be extremely useful in identifying fine‐scale genetic structures and providing insight into conservation management plans of this species.     

Isolation and characterization of microsatellite markers for Sabatia campestris (Gentianaceae), an Illinois state‐endangered plant

Sabatia campestris is a regionally endangered prairie plant. Eight polymorphic loci have been generated for S. campestris (Gentianaceae) using non‐enriched and enriched libraries. Polymorphism was quantified from an isolated population from central Illinois yielding mean observed and expected heterozygosities of 0.723 and 0.801, respectively. The number of alleles per locus for this population ranged from three to 25 with a median of 15.5. These genetic markers will be used to determine population genetic structure of Illinois populations as well as to estimate fine‐scale gene flow rates.     

Characterization of microsatellite markers for Sycoscapter nonpollinating fig wasps

We isolated 18 microsatellites from Sycoscapter australis, a nonpollinating fig wasp that develops in figs of Ficus macrophylla, and assessed their variability in 20 wasps. We further optimized nine of these loci for use in three other Sycoscapter species that develop in Ficus rubiginosa figs and assessed their variability in 47-140 wasps per species. These are the first microsatellites developed for nonpollinating fig wasps and show sufficient polymorphism to become important tools in evolutionary and genetical studies of Sycoscapter wasps.     

Isolation and characterization of microsatellite markers for Achyranthes bidentata (Amaranthaceae) using next-generation sequencing platform

Achyranthes bidentata Blume (Amaranthaceae) is a perennial herb that is widely distributed in India, Java, China, and Japan. The natural resources of A. bidentata in its geo-authentic product area have rapidly declined in recent years because of the over-collection of its roots. To devise adequate conservation and management strategies for this species, its genetic diversity and population structure should be characterized. Roche 454 pyrosequencing combined with magnetic bead enrichment was used to develop microsatellite markers for A. bidentata. A total of 903 microsatellite loci were identified from 42,004 individual sequence reads. One hundred microsatellite loci were selected to test the primer amplification efficiency across 16 individuals from two A. bidentata populations. Of these tested markers, 8 yielded polymorphic amplification products, 29 yielded single alleles. For polymorphic primer pairs, the number of alleles per locus ranged from 2 to 4, with an average of 2.75. The observed and expected heterozygosities ranged from 0.353 to 0.671 and 0.250 to 0.938, respectively. The inbreeding coefficient varied from −0.692 to 0.627. This set of markers will provide useful tools for examining genetic diversity and population structure, and aid in better understanding of the conservation of A. bidentata.