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Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements
No full textHorizontal gene transfer from viruses to eukaryotic cells is a pervasive phenomenon. Somatic viral integrations are linked to persistent viral infection whereas integrations into germline cells are maintained in host genomes by vertical transmission and may be co-opted for host functions. In the arboviral vector Aedes aegypti, an endogenous viral element from a nonretroviral RNA virus (nrEVE) was shown to produce PIWI-interacting RNAs (piRNAs) to limit infection with a cognate virus. Thus, nrEVEs may constitute a heritable, sequence-specific mechanism for antiviral immunity, analogous to piRNA-mediated silencing of transposable elements. Here, we combine population genomics and evolutionary approaches to analyse the genomic architecture of nrEVEs in A. aegypti. We conducted a genome-wide screen for adaptive nrEVEs and searched for novel population-specific nrEVEs in the genomes of 80 individual wild-caught mosquitoes from five geographical populations. We show a dynamic landscape of nrEVEs in mosquito genomes and identified five novel nrEVEs derived from two currently circulating viruses, providing evidence of the environmental-dependent modification of a piRNA cluster. Overall, our results show that virus endogenization events are complex with only a few nrEVEs contributing to adaptive evolution in A. aegypti
Baseline data for marine protected areas planning and fisheries monitoring : potential conflicts between recreational IUU and commercial fisheries in the proposed "Taza" MPA (Algeria, SW Mediterranean)
No full textNowadays, recreational fisheries (REC) have a great impact on marine ecosystems and create conflicts with other human coastal activities such as commercial small-scale fisheries (SSF). In the proposed "Taza" marine protected area (MPA) (Algeria, SW Mediterranean), recreational boat fishing is poorly regulated and its catches remain unmonitored. In addition, a significant number of REC fishers sell their catch illegally, an activity we could refer to as IUU (Illegal, Unreported, and Unregulated) fishing. This study is a good opportunity to evaluate the potential conflicts between recreational IUU and commercial fisheries and can be extremely valuable in terms of MPA planning and fisheries monitoring by providing baseline data for setting up sound fisheries management and conservation plans. Two fishing harbors are located near the proposed "Taza" MPA: Boudis and Ziama. Illegal REC boats from Ziama harbor were studied via a direct observation method of landings developed by the Ifremer (French Research Institute for Exploitation of the Sea). A comparison between illegal REC and SSF boats was highlighted in terms of catches and fishing effort. A total of 54 taxa belonging to 24 families were observed in the catches of the 32 recreational active boats in this harbor between May 2013 and April 2014. The proportion of the harvest attributed to illegal REC represented about 50% of the SSF harvest. Illegal REC in the proposed "Taza" MPA is an important socioeconomic activity which is intensively practiced throughout the year. From November to April, the mean catch was almost the same for both fishing categories. Strong competition between recreational and professional fishers for the natural resources was highlighted as 81% of the 54 caught taxa were present in the catches of both fishing categories (i.e. 44 taxa). Moreover, 4 species of high commercial value were caught exclusively by recreational fishers. Finally, the managers of the proposed "Taza" MPA must address and regulate all fishing activities and use the best available information in order to provide important benefits to marine ecosystems, fishers, and the local population
Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization
No full textEndogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated similar to 103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established similar to 53mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge. Jeremy Gauthier et al. present the chromosome scale assembly of the genome of the parasitic wasp C. congregata and show that bracovirus genes have colonized all ten chromosomes. Comparison with genome scaffolds of another wasp reveals a striking stability of these regions over similar to 53 million years, suggesting strong evolutionary constraints
Spatio-temporal dynamics of Plasmodium falciparum and Plasmodium vivax in French Guiana : 2005-2019
No full textAims: This study examines the dynamics of malaria as influenced by meteorological factors in French Guiana from 2005 to 2019. It explores spatial hotspots of malaria transmission and aims to determine the factors associated with variation of hotspots with time. Methods: Data for individual malaria cases came from the surveillance system of the Delocalized Centers for Prevention and Care (CDPS) (n = 17) from 2005-2019. Meteorological data was acquired from the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) database. The Box-Jenkins autoregressive integrated moving average (ARIMA) model tested stationarity of the time series, and the impact of meteorological indices (issued from principal component analysis-PCA) on malaria incidence was determined with a general additive model. Hotspot characterization was performed using spatial scan statistics. Results: The current sample includes 7050 eligible Plasmodium vivax (n = 4111) and Plasmodium falciparum (n = 2939) cases from health centers across French Guiana. The first and second PCA-derived meteorological components (maximum/minimum temperature/minimum humidity and maximum humidity, respectively) were significantly negatively correlated with total malaria incidence with a lag of one week and 10 days, respectively. Overall malaria incidence decreased across the time series until 2017 when incidence began to trend upwards. Hotspot characterization revealed a few health centers that exhibited spatial stability across the entire time series: Saint Georges de l'Oyapock and Antecume Pata for P. falciparum, and Saint Georges de l'Oyapock, Antecume Pata, Regina and Camopi for P. vivax. Conclusions: This study highlighted changing malaria incidence in French Guiana and the influences of meteorological factors on transmission. Many health centers showed spatial stability in transmission, albeit not temporal. Knowledge of the areas of high transmission as well as how and why transmission has changed over time can inform strategies to reduce the transmission of malaria in French Guiana. Hotspots should be further investigated to understand other influences on local transmission, which will help to facilitate elimination
Using scRNA-seq to identify transcriptional variation in the Malaria parasite ookinete stage
No full textThe crossing of the mosquito midgut epithelium by the malaria parasite motile ookinete form represents the most extreme population bottleneck in the parasite life cycle and is a prime target for transmission blocking strategies. However, we have little understanding of the clonal variation that exists in a population of ookinetes in the vector, partially because the parasites are difficult to access and are found in low numbers. Within a vector, variation may result as a response to specific environmental cues or may exist independent of those cues as a potential bet-hedging strategy. Here we use single-cell RNA-seq to profile transcriptional variation in Plasmodium berghei ookinetes across different vector species, and between and within individual midguts. We then compare our results to low-input transcriptomes from individual Anopheles coluzzii midguts infected with the human malaria parasite Plasmodium falciparum. Although the vast majority of transcriptional changes in ookinetes are driven by development, we have identified candidate genes that may be responding to environmental cues or are clonally variant within a population. Our results illustrate the value of single-cell and low-input technologies in understanding clonal variation of parasite populations
Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission
No full textBackground Fruit abscission depends on cell separation that occurs within specialized cell layers that constitute an abscission zone (AZ). To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Results Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. Conclusions The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process
Managing and monitoring genetic isolation and local adaptation of endemic and introduced Cotesia sesamiae for the biological control of the cereal stemborer Busseola fusca in Cameroon
No full textThe success of biological bontrol (BC) introductions can be enhanced by considering theory and knowledge of biological systems. The gregarious braconid parasitoid Cotesia sesamiae (Cameroon) is one of the best studied biological control agent from the perspective of molecular ecology. Its evolutionary adaptation to the target host involves symbiotic partners. Polydnaviruses are responsible for immune and developmental adaptations whereas Wolbachia bacteria may reinforce this local adaptation though genetic isolation mechanisms. The noctuid Busseola fusca is a major stemborer pest of maize in sub-Saharan Africa. In contrast to eastern Africa, C. sesamiae is rarely found on B. fusca in western Africa. It is however often obtained from other stemborer species feeding on wild grasses. A biological control project was launched in 2006-2007 by introducing to Cameroon seven crosses of Kenyan populations of C. sesamiae collected in different ecozones. They included populations adapted to B. fusca that develop on maize as well as populations adapted to other hosts feeding on wild plants to allow carryover between cropping seasons. Wolbachia strains responsible for cytoplasmic reproductive incompatibilities with endemic strains were included in the crosses to limit genetic exchanges between introduced and endemic C. sesamiae and preserve genetic adaptation to B. fusca of the introduced populations, while at the same time preserving their ability to survive on wild plants. Six post release surveys were carried out on maize from 2007 to 2013, and on wild grasses in 2013. A total of 393 C. sesamiae individuals, each from one cocoon mass, were genotyped for 11 microsatellite loci. Multidimensional scaling analysis, STRUCTURE and GENE CLASS analyses assigned almost all the parasitoids recovered from maize to those introduced from Kenya. The introduced strains were also recovered from wild host plants with little genetic exchanges with endemics. Each population remained strongly associated with its original Wolbachia component, suggesting that Wolbachia may contribute to genetic isolation between endemics and introduced populations in wild host plants when maize is absent, thereby conciliating biological control success and safety
Environmental drivers of mesophotic echinoderm assemblages of the Southeastern Pacific Ocean
No full textMesophotic ecosystems (50-400 m depth) of the southeastern Pacific have rarely been studied because of the logistical challenges in sampling across this remote zone. This study assessed how oxygen concentrations and other environmental predictors explain variation in echinoderm assemblages at these mesophotic systems, where this group is among the predominant fauna. We compiled data on echinoderm taxa at 91 sampling stations, from historical and recent surveys (between 1950 and 2019), covering a longitudinal gradient of approximately 3,700 km along with the Nazca, Salas y Gomez, and Juan Fernandez ridges. Uni- and multivariate model-based tools were applied to analyze the patterns of benthic fauna in relation to environmental factors. Our results indicate a significant positive relationship between echinoderm species richness and depth, oxygen, and salinity. Changes in echinoderm community composition were significantly explained by oxygen, longitude, and chlorophyll-a. We observed notable species turnovers at similar to 101 and similar to 86 degrees W, where assemblages tend to be more variable across stations. This turnover possibly reflects the effects of physical barriers to dispersion (e.g., currents) and habitat changes. Echinoderm assemblages observed around Easter and Desventuradas Islands presented a high occurrence of potentially endemic taxa and distinct species assemblages. This study is the first to assess the structure of mesophotic echinoderm assemblages of the southeastern Pacific Ocean along a large spatial scale. The information reported here could help design appropriate management tools for the vast, recently created, marine protected areas in the southeastern Pacific
Sea state from single optical images : a methodology to derive wind-generated ocean waves from cameras, drones and satellites
No full textSea state is a key variable in ocean and coastal dynamics. The sea state is either sparsely measured by wave buoys and satellites or modelled over large scales. Only a few attempts have been devoted to sea state measurements covering a large domain; in particular its estimation from optical images. With optical technologies becoming omnipresent, optical images offer incomparable spatial resolution from diverse sensors such as shore-based cameras, airborne drones (unmanned aerial vehicles/UAVs), or satellites. Here, we present a standalone methodology to derive the water surface elevation anomaly induced by wind-generated ocean waves from optical imagery. The methodology was tested on drone and satellite images and compared against ground truth. The results show a clear dependence on the relative azimuth view angle in relation to the wave crest. A simple correction is proposed to overcome this bias. Overall, the presented methodology offers a practical way of estimating ocean waves for a wide range of applications