Novel microsatellite loci for Sebaea aurea (Gentianaceae) and cross-amplification in related species.

Premise of the study: Microsatellite loci were developed in Sebaea aurea (Gentianaceae) to investigate the functional role of diplostigmaty (i.e., the presence of additional stigmas along the style). Methods and Results: One hundred seventy-four and 180 microsatellite loci were isolated through 454 shotgun sequencing of genomic and microsatellite-enriched DNA libraries, respectively. Sixteen polymorphic microsatellite loci were characterized, and 12 of them were selected to genotype individuals from two populations. Microsatellite amplification was conducted in two multiplex groups, each containing six microsatellite loci. Cross-species amplification was tested in seven other species of Sebaea. The 12 novel microsatellite loci amplified only in the two most closely related species to S. aurea (i.e., S. ambigua and S. minutiflora) and were also polymorphic in these two species. Conclusions: These results demonstrate the usefulness of this set of newly developed microsatellite loci to investigate the mating system and population genetic structure in S. aurea and related species

Genetic differentiation of Anopheles gambiae populations from East and West Africa : comparison of microsatellite and allozyme loci

Genetic variation of #Anopheles gambiae$ was analysed to assess interpopulation divergence over a 6000 km distance using short tandem repeat (microsatellite) loci and allozyme loci. Differentiation of populations from Kenya and Senegal measured by allele length variation at five microsatellite loci was compared with estimates calculated from published data on six allozyme loci (Miles, 1978). The average Wright's F(ST) of microsatellite loci (0.016) was lower than that of allozymes (0.036). Slatkin's R(ST) values for microsatellite loci were generally higher than their F(ST) values, but the average R(ST) value was virtually identical (0.036) to the average allozyme F(ST). These low estimates of differentiation correspond to an effective migration index (Nm) larger than 3, suggesting that gene flow across the continent is only weakly restricted. Polymorphism of microsatellite loci was significantly higher than that of allozymes, probably because the former experience considerably higher mutation rates. That microsatellite loci did not measure greater interpopulation divergence than allozyme loci suggested constraints on microsatellite evolution. Alternatively, extensive mosquito dispersal, aided by human transportation during the last century, better explains the low differentiation and the similarity of estimates derived from both types of genetic markers. (Résumé d'auteur

Novel microsatellite loci for Sebaea aurea (Gentianaceae) and cross-amplification in related species.

[Premise of the study] Microsatellite loci were developed in Sebaea aurea (Gentianaceae) to investigate the functional role of diplostigmaty (i.e., the presence of additional stigmas along the style).[Methods and Results] One hundred seventy-four and 180 microsatellite loci were isolated through 454 shotgun sequencing of genomic and microsatellite-enriched DNA libraries, respectively. Sixteen polymorphic microsatellite loci were characterized, and 12 of them were selected to genotype individuals from two populations. Microsatellite amplifi cation was conducted in two multiplex groups, each containing six microsatellite loci. Cross-species amplifi cation was tested in seven other species of Sebaea . The 12 novel microsatellite loci amplifi ed only in the two most closely related species to S. aurea (i.e., S. ambigua and S. minutifl ora ) and were also polymorphic in these two species.[Conclusions] These results demonstrate the usefulness of this set of newly developed microsatellite loci to investigate the mating system and population genetic structure in S. aurea and related species.We acknowledge grants to J.K. from the Swiss National Science Foundation (PA00P3_129140) and the Velux Stiftung (project no. 679) and to J.G.S.-M. from a postdoctoral research contract “Ramón y Cajal” from the Ministerio de Ciencia e Innovación (MICINN), Spain.Peer Reviewe

Using eggshell membranes as a DNA source for population genetic research

In the context of population genetic research, a faster and less invasive method of DNA sampling would allow large-scale assessments of genetic diversity and genetic differentiation with the help of volunteer observers. The aim of this study was to investigate the usefulness of eggshell membranes as a DNA source for population genetic research, by addressing eggshell membrane DNA quality, degeneration and cross-contamination. To this end, a comparison was made with blood-derived DNA samples. We have demonstrated 100% successful DNA extraction from post-hatched Black-tailed Godwit (Limosa limosa) eggshell membranes as well as from blood samples. Using 11 microsatellite loci, DNA amplification success was 99.1% for eggshell membranes and 97.7% for blood samples. Genetic information within eggshell membrane DNA in comparison to blood DNA was not affected (F-ST = -0.01735, P = 0.999) by degeneration or possible cross-contamination. Furthermore, neither degeneration nor cross-contamination was apparent in total genotypic comparison of eggshell membrane DNA and blood sample DNA. Our research clearly illustrates that eggshell membranes can be used for population genetic research

Development of Multiple Polymorphic Microsatellite Markers for Ceratina calcarata (Hymenoptera: Apidae) Using Genome-Wide Analysis

The small carpenter bee, Ceratina calcarata (Robertson), is a widespread native pollinator across eastern North America. The behavioral ecology and nesting biology of C. calcarata has been relatively well-studied and the species is emerging as a model organism for both native pollinator and social evolution research. C. calcarata is subsocial: reproductively mature females provide extended maternal care to their brood. As such, studies of C. calcarata may also reveal patterns of relatedness and demography unique to primitively social Hymenoptera. Here, we present 21 microsatellite loci, isolated from the recently completed C. calcarata genome. Screening in 39 individuals across their distribution revealed that no loci were in linkage disequilibrium, nor did any deviate significantly from Hardy-Weinberg following sequential Bonferroni correction. Allele count ranged from 2 to 14, and observed and expected heterozygosities ranged from 0.08 to 0.82 (mean 0.47) and 0.26 to 0.88 (mean 0.56), respectively. These markers will enable studies of population-wide genetic structuring across C. calcarata’s distribution. Such tools will also allow for exploration of between and within-colony relatedness in this subsocial native pollinator

Identification and validation of microsatellite markers in strawberry tree (Arbutusunedo L.)

Strawberry tree (Arbutus unedo L.), an evergreen shrub/small tree of the family Ericaceae, is a main constituent of the Mediterranean basin flora; although it is also found in southwestern Prance, Macaronesia, and Ireland. The small fruits are edible but mostly used for preparation of preserves and jams, and for liquors such as the Portuguese traditional "aguardente de medronho". Traditionally cultivated by small farmers, often in consociation with Quercus sp., strawberry tree is presently emerging as a new important fruit crop cultivated in large orchards by modern export-oriented enterprises. This change of paradigm requires a growing role of plant breeding, upstream of the production process. Genomic tools for this species are mostly limited to the chloroplast genome sequence and to genomic data described in this work. In order to identify strawberry tree microsatellite (SSR) loci we performed partial genome next-generation sequencing using the Ion Torrent technology. The sequenced similar to 24.6M nucleotides resulted in the identification of 1185 microsatellite markers mostly constituted by dinucleotide motifs. The relative amount of microsatellite dinucleotide motifs (AG/CT - 71.7%, AC/GT - 20.5%, AT/AT - 2.9%, and CG/CG - 0.3%) is similar to the one observed in other Ericaceae species. Among a tested sample of 40 SSR primer pairs, 20 amplified well-defined PCR products, 12 (30%) were validated as polymorphic. Used in our collaborative project for molecular identification of selected and improved clones, the identified SSR loci constitute a strong tool for a large panoply of applied and fundamental studies of this emerging fruit crop.Pluriannual Funding Program of the Portuguese National Foundation for Science and Technologyinfo:eu-repo/semantics/publishedVersio

Characterization of Mauritius parakeet (Psittacula eques) microsatellite loci and their cross-utility in other parrots (Psittacidae, Aves).

We characterized 21 polymorphic microsatellite loci in the endangered Mauritius parakeet (Psittacula eques). Loci were isolated from a Mauritius parakeet genomic library that had been enriched separately for eight different repeat motifs. Loci were characterized in up to 43 putatively unrelated Mauritius parakeets from a single population inhabiting the Black River Gorges National Park, Mauritius. Each locus displayed between three and nine alleles, with the observed heterozygosity ranging between 0.39 and 0.96. All loci were tested in 10 other parrot species. Despite testing few individuals, between seven and 21 loci were polymorphic in each of seven species tested

Cross-amplification and characterization of polymorphic microsatellite markers from Acacia (Senegalia) mellifera and Acacia brevispica to Acacia senegal (L.) Willd.

Seven polymorphic microsatellite markers isolated from Acacia brevispica and Acacia mellifera were successfully cross-amplified in Acacia senegal. The loci were surveyed for polymorphism using 30 samples. Allelic diversity ranged from 4 (Ame02, Ab06 and Ab18) to 13 (Ab26) per locus. The expected heterozygosity (HE) ranged from 0.543 (Ame02) to 0.868 (Ab26) while observed heterozygosity (HO) ranged from 0.516 (Ame05) to 0.800 (Ame03). Cross amplification of these loci represents a potential source of co-dominant marker and will be useful in the study of genetic diversity, structure, gene flow and breeding systems of this important Acacia species

Comparative population structure of <i>Plasmodium malariae</i> and <i>Plasmodium falciparum</i> under different transmission settings in Malawi

&lt;b&gt;Background:&lt;/b&gt; Described here is the first population genetic study of Plasmodium malariae, the causative agent of quartan malaria. Although not as deadly as Plasmodium falciparum, P. malariae is more common than previously thought, and is frequently in sympatry and co-infection with P. falciparum, making its study increasingly important. This study compares the population parameters of the two species in two districts of Malawi with different malaria transmission patterns - one seasonal, one perennial - to explore the effects of transmission on population structures. &lt;BR/&gt; &lt;b&gt;Methods:&lt;/b&gt; Six species-specific microsatellite markers were used to analyse 257 P. malariae samples and 257 P. falciparum samples matched for age, gender and village of residence. Allele sizes were scored to within 2 bp for each locus and haplotypes were constructed from dominant alleles in multiple infections. Analysis of multiplicity of infection (MOI), population differentiation, clustering of haplotypes and linkage disequilibrium was performed for both species. Regression analyses were used to determine association of MOI measurements with clinical malaria parameters. &lt;BR/&gt; &lt;b&gt;Results:&lt;/b&gt; Multiple-genotype infections within each species were common in both districts, accounting for 86.0% of P. falciparum and 73.2% of P. malariae infections and did not differ significantly with transmission setting. Mean MOI of P. falciparum was increased under perennial transmission compared with seasonal (3.14 vs 2.59, p = 0.008) and was greater in children compared with adults. In contrast, P. malariae mean MOI was similar between transmission settings (2.12 vs 2.11) and there was no difference between children and adults. Population differentiation showed no significant differences between villages or districts for either species. There was no evidence of geographical clustering of haplotypes. Linkage disequilibrium amongst loci was found only for P. falciparum samples from the seasonal transmission setting. &lt;BR/&gt; &lt;b&gt;Conclusions:&lt;/b&gt; The extent of similarity between P. falciparum and P. malariae population structure described by the high level of multiple infection, the lack of significant population differentiation or haplotype clustering and lack of linkage disequilibrium is surprising given the differences in the biological features of these species that suggest a reduced potential for out-crossing and transmission in P. malariae. The absence of a rise in P. malariae MOI with increased transmission or a reduction in MOI with age could be explained by differences in the duration of infection or degree of immunity compared to P. falciparum