Recombination and dynamics of transposable elements in natural populations. A drosophilist’s view

The concept of the tight link between crossing over and the dynamics of transposable elements is presented. The behavior of transposable elements influences the processes of homologous recombination, both at the moment of activation and as a result the changes in a genome caused by active transposition of the autonomous nucleotide sequences

Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect

Social insects provide systems for studying epigenetic regulation of phenotypes, particularly with respect to differentiation of reproductive and worker castes, which typically arise from a common genetic background. The role of gene expression in caste specialization has been extensively studied, but the role of DNA methylation remains controversial. Here, we perform well replicated, integrated analyses of DNA methylation and gene expression in brains of an ant (Formica exsecta) with distinct female castes using traditional approaches (tests of differential methylation) combined with a novel approach (analysis of co-expression and co-methylation networks). We found differences in expression and methylation profiles between workers and queens at different life stages, as well as some overlap between DNA methylation and expression at the functional level. Large portions of the transcriptome and methylome are organized into "modules" of genes, some significantly associated with phenotypic traits of castes and developmental stages. Several gene co-expression modules are preserved in co-methylation networks, consistent with possible regulation of caste-specific gene expression by DNA methylation. Surprisingly, brain co-expression modules were highly preserved when compared with a previous study that examined whole-body co-expression patterns in 16 ant species, suggesting that these modules are evolutionarily conserved and for specific functions in various tissues. Altogether, these results suggest that DNA methylation participates in regulation of caste specialization and age-related physiological changes in social insects.Peer reviewe

Assessment of Colobanthus quitensis genetic polymorphism from the Argentine Islands region (maritime Antarctic) by actin, α- and γ-tubulin gene intron analysis

Colobanthus quitensis is one of the two angiosperm plant species commonly spread in the Antarctic. The species has been extensively analyzed at morphological, anatomical and physiological levels, but information regarding its genetic vari-ability remains limited. The aim of the study was to identify molecular genetic differences between C. quitensis populations in one of the Antarctic localities, the Argentine Islands region by estimating the intron length polymorphism of actin, α- and γ-tubulin genes. Samples of C. quitensis from different Antarctic natural populations were collected during the season of the 24th and previous Ukrainian Antarctic expeditions. Total DNA was isolated using the QIAGEN DNeasy Plant Mini Kit. The polymerase chain reaction was carried out with our own degenerate primers. The resulting amplicons were separated and visualized using polyacrylamide gel electrophoresis followed by silver nitrate staining. Molecular genetic analysis of natural populations of C. quitensis was performed using three DNA-marker systems based on the detection of intron length polymor-phism of actin, α- and γ-tubulin genes. A low level of genetic polymorphism of C. quitensis in the studied region by these types of markers was established. By assessing the intron length polymorphism of actin genes of the studied C. quitensis populations it was possible to establish that the populations of Skua Island had unique amplicons characteristic only for this location. This indicates the possibility of further use of the analysis of intron length polymorphism of actin genes for the study of the molecu-lar genetic diversity of the Antarctic pearlwort. At the same time, the results of analysis of the intron length polymorphism of α- and γ-tubulin genes induce selection of more specific primers, taking into account the structure of the C. quitensis genome. C. quitensis in the study region has a low level of genetic variability in intron length polymorphism of actin, α- and γ-tubulin genes. Overall, the results indicate that DNA markers based on gene structure analysis of highly conserved cytoskeletal pro-teins, namely, actin, α- and γ-tubulin, as additional sources of information, can be used for molecular genetic analysis of C. quitensis populations in the Antarctic

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.We thank four reviewers and the handling editor for helpful comments on previous versions of our manuscript. We are grateful to the members of the DrosEU and DrosRTEC consortia for their long-standing support, collaboration, and for discussion. DrosEU was funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). M.K. was supported by the Austrian Science Foundation (grant no. FWF P32275); J.G. by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); T.F. by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of Münster; AOB by the National Institutes of Health (R35 GM119686); M.K. by Academy of Finland grant 322980; V.L. by Danish Natural Science Research Council (FNU) (grant no. 4002-00113B); FS Deutsche Forschungsgemeinschaft (DFG) (grant no. STA1154/4-1), Project 408908608; J.P. by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; A.U. by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) (grant no. 1737/17); M.S.V., M.S.R. and M.J. by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); A.P., K.E. and M.T. by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007); and TM NSERC grant RGPIN-2018-05551. The authors acknowledge Research Computing at The University of Virginia for providing computational resources and technical support that have contributed to the results reported within this publication (https://rc.virginia.edu, last accessed September 6, 2021)

Reproductive success of Drosophila melanogaster: natural populations from radioactively contaminated territori

Drosophila individuals were collected in autumn 2006 from sites in Ukraine with different levels of radioactive contamination. Flies were sampled near the cooling pond of Chernobyl Nuclear Power Plant with a radioactive background of 2100 µR/h, the city of Chernobyl (100 µ R/h), in Polesskoe (50 µR/h), Lubny (16 µR/h), Uman (16 µR/h), Piryatin (15 µR/h), Odessa (14 µR/h) and Kyiv (13 µR/h). The fecundity, scored as the average number of offspring produced by F1 females, was obtained for each population. Fecundity varied from 19.06±3.87 (Chernobyl cooling pond) to 42.93±3.77 (Polesskoe). The lowest fecundity was seen in the populations from the most radioactively contaminated sites. An exception was Polesskoe, whose larvae fed on substrate derived from less polluted areas. There was no relationship between fecundity and background contamination levels for populations from the relatively uncontaminated sites, as they varied by only 3 µR/h. Laboratory strains during 20 generations lived under chronic exposure (dose rate 1,2 12 mR/h ) in terms of mini ?-field. The doses accumulated for 20 generation are in interval 0,1- 1 Gy. Fecundity index in control of Conton-S strain was 60,54±1,9, higher than in natural populations. At the same time the fecundity index for Conton-S after chronic exposure with dose rate 12mR/h decline to 24,87±1,36. Active mobile genetic elements are known to cause gonad reduction in Drosophilids. Gonad reduction varied from 0 (which cannot be considered, as it less than 1%) to 14±0.5% in our populations. These levels of gonad reduction suggest mobile genetic elements are not active in any of the studied populations. Therefore the observed decrease in fecundity in populations from the city of Chernobyl and near the cooling pond of the Chernobyl reactor is not likely related to any elevated activity of mobile elements

Polimorphism of β -specific carboxylesterases in the populations of Drosophila melanogaster of Ukraine

As a result of radioactive contamination after Chernobyl disaster, there are a lot of animals that live in the condition of chronic radiation in the Ukraine. One of the most important consequences of the radioactive effect is a change in the frequency of different alleles and genotypes in populations. Therefore, we have investigated the frequency of different allotypes of β -specific carboxylesterases (βEst) in different populations of Drosophila melanogaster. One of them has been chosen from natural populations in southern Ukraine (Odesskaya) and three others from radioactive contamination territories (1-3). Using the method of vertical-plate alkaline electrophoresis in polyacrylamid gel (7%) we separated ferment-containing buffer-triton tissue extracts of imago of D. melanogaster (15 flies per population). After the electrophoresis, the gel was exposed to the incubatory medium (pH 7,4), that contained α- and β-naphtilacetates and prussian blue. The level of activity of some esterase was determined by controlling the intensity of coloring of the different fractions, which correspond to the ferment localization in gel, and which contain products of azocoupling of naphtols and diazonium. Using electrophoresis we have shown that there were two allelic forms of solubility β -specific carboxylesterases in the extracts we have obtained from fruit flies from different populations: fast form (F-type) and slow form (S-type) with Rf indexes 350 and 380 respectively. S-allozyme has not been detected in the population Odesskaya and 2 and thus the frequency of F-allozymes in this groups reaches 100%. In the population 1 the frequency of S-allele were 70,7% and in this respect the frequency of F-allele were equal to 29,3%. Whereas in the population 3, which was obtained from the most contaminated territory, the frequency of F-allele (73,0%) was significantly higher than the one of S-allele (25,8%). Interestingly, all F-alleles were in heterozygote condition in this group. Also, in all cases the activities of S-allozymes were higher than of F allozymes. For instance, in the population 1 the coverage activity of S-allozymes of B-specific carboxylesterases was 1,025±0,096 and for F-allozymes the respective index was 0,710±0,088 (enzymes activity show in relative units (indexes) of optical density, calculated by a special PC programme ANAIS). Equal indexes in the population 3 were 1,187±0,124 and 0,858±0,072 respectively. More importantly, the activities of S-allozymes in the population Odesskaya were in one and a half fold higher than in other populations and obviously this is a special peculiarity of this group of D. melanogaster

Bacteria Associated with the Antarctic Endemic Insect Belgica antarctica Jacobs (Diptera Chironomidae)

International audienceInsects are one of the most successful groups of multicellular organisms with more than a million species. Among them, there is Belgica antarctica Jacobs (Diptera Chironomidae) representing an endemic species of Antarctica that exists under extremely cold conditions. A significant number of microorganisms colonize most species of insects resulting in symbiotic interaction, which may improve the adaptability of a host organism to cold conditions. Using PCR and metagenomic analysis, it has been demonstrated that endosymbiotic bacteria Spiroplasma and Wolbachia seem to be absent in Belgica antarctica. Nevertheless, 14 species of bacteria have been revealed that can be potentially associated with Belgica antarctica and/or with the substrate where this species lives by screening the whole-genome sequences available in open databases. To ascertain the constant association of identified microorganisms with Belgica antarctica and their possible preference to this species, it is necessary to perform further analysis