Prejudices against Microsatellite Studies and How to Resist Them

Russian Journal of Genetics - In this article, we summarize the basic concepts and techniques widely used in microsatellite studies. We describe briefly the main stages of the work and provide...     

Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data

Insertions and deletions (indels) in human genomes are associated with a wide range of phenotypes, including various clinical disorders. High-throughput, next generation sequencing (NGS) technologies enable the detection of short genetic variants, such as single nucleotide variants (SNVs) and indels. However, the variant calling accuracy for indels remains considerably lower than for SNVs. Here we present a comparative study of the performance of variant calling tools for indel calling, evaluated with a wide repertoire of NGS datasets. While there is no single optimal tool to suit all circumstances, our results demonstrate that the choice of variant calling tool greatly impacts the precision and recall of indel calling. Furthermore, to reliably detect indels, it is essential to choose NGS technologies that offer a long read length and high coverage coupled with specific variant calling tools.     

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate,life-history traits and anthropogenic factors

We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5–20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.     

On the estimation of the influence of the character of insect pollinators movements on the pollen transfer dynamics

The pattern of pollinator movements determines the dynamics of the pollen transfer between zoophilic plants. The structure of plant populations depends on this aspect of the pollinator foraging behavior. A new method for the estimation of the rate of moving away from an object was used for a more precise determination of the distance at which pollinators transfer pollen. The method is based on the measuring of distances covered by pollinators per several flights. The highest rate was found in hoverflies (Diptera, Syrphidae). Butterflies (Pieris brassicae) play an insignificant role in long-distance pollen transfers due to their circular movements.     

Genomic exaptation enables <Emphasis Type="Italic">Lasius niger</Emphasis> adaptation to urban environments

Background

The world is rapidly urbanizing, and only a subset of species are able to succeed in stressful city environments. Efficient genome-enabled stress response appears to be a likely prerequisite for urban adaptation. Despite the important role ants play in the ecosytem, only the genomes of ~13 have been sequenced so far. Here, we present the draft genome assembly of the black garden ant Lasius niger – the most successful urban inhabitant of all ants – and we compare it with the genomes of other ant species, including the closely related Camponotus floridanus.

Results

Sequences from 272 M Illumina reads were assembled into 41,406 contigs with total length of 245 MB, and N50 of 16,382 bp, similar to other ant genome assemblies enabling comparative genomic analysis. Remarkably, the predicted proteome of L. niger is significantly enriched relative to other ant genomes in terms of abundance of domains involved in nucleic acid binding, DNA repair, and nucleotidyl transferase activity, reflecting transposable element proliferation and a likely genomic response. With respect to environmental stress, we note a proliferation of various detoxification genes, including glutatione-S-transferases and those in the cytochrome P450 families. Notably, the CYP9 family is highly expanded with 19 complete and 21 nearly complete members - over twice as many compared to other ants. This family exhibits the signatures of strong directional selection, with eleven positively selected positions in ligand-binding pockets of enzymes. Gene family contraction was detected for several components of the olfactory system, accompanied by instances of both directional selection and relaxation.

Conclusions

Our results suggest that the success of L. niger in urbanized areas may be the result of fortuitous coincidence of several factors, including the expansion of the CYP9 cytochrome family due to coevolution with parasitic fungi, the diversification of DNA repair systems as an answer to proliferation of retroelements, and the reduction of olfactory system and behavioral preadaptations from non-territorial subdominant life strategies found in natural environments. Diversification of cytochromes and DNA repair systems along with reduced odorant communication are the basis of L. niger pollutant resistance and polyphagy, while non-territorial and mobilization strategies allows more efficient exploitation of large but patchy food sources.

     

Is it possible to prove the existence of an aging program by quantitative analysis of mortality dynamics?

Accumulation of various types of lesions in the course of aging increases an organism’s vulnerability and results in a monotonous elevation of mortality rate, irrespective of the position of a species on the evolutionary tree. Stroustrup et al. (Nature, 530, 103–107) [1] showed in 2016 that in the nematode Caenorhabditis elegans, longevity-altering factors (e.g. oxidative stress, temperature, or diet) do not change the shape of the survival curve, but either stretch or shrink it along the time axis, which the authors attributed to the existence of an “aging program”. Modification of the accelerated failure time model by Stroustrup et al. uses temporal scaling as a basic approach for distinguishing between quantitative and qualitative changes in aging dynamics. Thus we analyzed data on the effects of various longevity-increasing genetic manipulations in flies, worms, and mice and used several models to choose a theory that would best fit the experimental results. The possibility to identify the moment of switch from a mortality-governing pathway to some other pathways might be useful for testing geroprotective drugs. In this work, we discuss this and other aspects of temporal scaling.     

Comparison of the pollen content on the body and in the gut of hoverflies (Diptera,Syrphidae)

We analyzed the pollen content in the gut and on the body of hoverflies (Diptera: Syrphidae), mostly from three genera (Eristalis, Syrphus s. l., and Sphaerophoria) that visited flowers of two jointly flowering species of Apiaceae with indistinguishable pollen (Anthriscus sylvestris and Aegopodium podagraria) and of Bunias orientalis (Brassicaceae). Pollen compositions depended on the plant from which the flies were collected rather than on the insect genus. At the same time, individual preferences of the studied flies to food plant species were confirmed. The pollen compositions in the gut and on the body were weakly correlated. Two possible reasons for such a weak correlation are discussed: individual differences in the fly feeding habits and different time of pollen preservation in the gut and on the body.     

Movement patterns of the main insect pollinator groups during foraging on generalized plants

Movements of pollinators in generalized plant-pollinator systems were investigated. Some species of insects, unlike the majority of the species studied, are shown to prefer areas with sparse plant cover. Thus, the composition of pollinators depends on the density of plant patches and can vary even within a distance of several meters. Within large plant patches, insects usually forage in a small plot and then move to another one.