Brain transcriptomes of honey bees (Apis mellifera) experimentally infected by two pathogens: Black queen cell virus and Nosema ceranae.

This is the final version of the article. Available from Elsevier via the DOI in this record.Regulation of gene expression in the brain plays an important role in behavioral plasticity and decision making in response to external stimuli. However, both can be severely affected by environmental factors, such as parasites and pathogens. In honey bees, the emergence and re-emergence of pathogens and potential for pathogen co-infection and interaction have been suggested as major components that significantly impaired social behavior and survival. To understand how the honey bee is affected and responds to interacting pathogens, we co-infected workers with two prevalent pathogens of different nature, the positive single strand RNA virus Black queen cell virus (BQCV), and the Microsporidia Nosema ceranae, and explored gene expression changes in brains upon single infections and co-infections. Our data provide an important resource for research on honey bee diseases, and more generally on insect host-pathogen and pathogen-pathogen interactions. Raw and processed data are publicly available in the NCBI/GEO database: (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE81664.Sequencing was performed thanks to the EU-funded 7th Framework project BEE DOC, Grant Agreement 244956. The authors thank Maureen Labarussias for technical support during bee experiments and preparation for sequencing

Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress

To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70–84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress

The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps.

Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophyletic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history

Differential root transcriptomics in a polypoloid non-model crop: the importance of respiration during osmotic stress

To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70-84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress.status: publishe

Transcriptomic profiling in Musa: a look into processes affected by mild osmotic stress in the root tip

Drought stress is one of the major abiotic factors limiting banana (Musa) production. Even mild-drought conditions are responsible for considerable yield losses. We performed large-scale transcriptome sequencing using Illumina technology on root tissue of three triploid genotypes representing well known cultivars and focused on the identification of genes with an altered expression pattern under mild osmotic stress (3 days after 5% PEG treatment). In total, 18 cDNA libraries were sequenced producing around 568 million high quality reads, of which 70-84% were mapped to the diploid reference genome (D’Hont et al., 2012). Through uni-/multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present a panorama of the general processes affected by mild osmotic stress in the root tip, although we observe a bias towards glycolysis and fermentation. We hypothesize that in this fast growing and oxygen demanding tissue, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To validate the mRNA-seq results, a subset of twenty up-regulated genes were further analyzed at three different time points (6 hours, 3 days and 7 days) in an independent PEG experiment. Overall, the identification and annotation of this set of genes constitutes a step ahead to understand the complex network of root responses to osmotic (drought) stress

Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner

International audienc

Prostaglandin D2 acts through the Dp2 receptor to influence male germ cell differentiation in the foetal mouse testis

International audienceThrough intercellular signalling, the somatic compartment of the foetal testis is able to program primordial germ cells to undergo spermatogenesis.Fibroblastgrowthfactor9 and several members of the transforming growth factorβ superfamily are involved in this process in the foetal testis, counteracting the induction of meiosis byretinoic acid and activating germinal mitotic arrest. Here, using in vitro and in vivo approaches, we show that prostaglandin D2(PGD2), which is produced through both L-Pgds and H-Pgds enzymatic activities in the somatic and germ cell compartments of the foetal testis, plays a role in mitotic arrest in male germ cells by activating the expression and nuclear localization of the CDK inhibitor p21 Cip1 and by repressing pluripotency markers. We show that PGD2 acts through its Dp2 receptor, at least in part through direct effects in germ cells, and contributes to the proper differentiation of male germ cells through the upregulation of the master gene Nanos2. Our data identify PGD2 signalling as an early pathway that acts in both paracrine and autocrine manners, and contributes to thedifferentiation of germ cells in the foetal testis

The evolutionary history of Chalcid wasps (Hymenoptera)

International audienceChalcidoidea is one of the most species-rich and morphologically diverse superfamily of Hymenoptera. Chalcid wasps encompass important ecological role by regulating insect populations in most ecosystems of the earth. However, the evolutionary history of the superfamily is still poorly understood. In our study, we used more than 1000 Ultra-Conserved Elements (UCEs) to reconstruct higher-level relationships within Chalcidoidea. We included members of all major lineages (701 species (692 ingroups + 9 outgroups), representing 23 families of chalcids, 93 subfamilies, 154 tribes and 582 genera). We will discuss, our main results and the difficulties we had to resolve the backbone of the chalcid radiation. Among the 23 families represented, 17 were recovered monophyletic (#75%); 6 poly- or paraphyletic (namely Chalcididae, Aphelinidae, Eulophidae, and Perilampidae; two families literally exploded respectively in 6 and 25 independent clades (Eupelmidae and Pteromalidae, the garbage can of the superfamily). Finally, we investigated the timing and patterns of diversification of chalcids wasps and propose a new time-scale for the evolution of the superfamily

The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps

Cruaud, Astrid, Rasplus, Jean-Yves, Zha, Junxia, Burks, Roger, Delvare, Ǵerard, Fusu, Lucian, Gumovsky, Alex, Huber, John T., Jan̆sta, Petr, Mitroiu, Mircea-Dan, Noyes, John S., Noort, Simon van, Baker, Austin, Bohmova, Julie, Baur, Hannes, Blaimer, Bonnie B., Brady, Sean G., Bubeńıkova, Kristyna, Chartois, Marguerite, Copeland, Robert S., Papilloud, Natalie Dale-Skey, Molin, Ana Dal, Dominguez, Chrysalyn, Gebiola, Marco, Guerrieri, Emilio, Kresslein, Robert L., Krogmann, Lars, Lemmon, Emily, Murray, Elizabeth A., Nidelet, Sabine, Nieves-Aldrey, Jośe Luis (2023): The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps. Cladistics 2023: 1-30, DOI: 10.1111/cla.1256

Fig. 3 in The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps

Fig. 3. Collapsed summary cladograms. Combined AHE (exonsAA) and UCE (UCEs90-25) results for 433 taxa, 2054 loci including 103 395 AA +180 711 nucleotide sites. Results of IQ-TREE concatenated analysis with one partition for each type of data (exonsAA vs. UCEs90-25). SHaLRT/UFBoot/gCF/sCF are indicated at nodes. Clades were collapsed to higher level groups (family, subfamily, tribe). Colours are meant to allow for comparisons between trees. Vertical bars represent similar clade relationships for the analyses of IQ-TREE: UCEs90-25 (UCE407), exonsAA (AHE414), AHE520AA; parsimony: combined (COM433), UCEs90-25 (UCE407), exonsAA (AHE414), AHE520AA; Munro et al. (2011; 720 taxa); Heraty et al. (2013; 300 taxa). Vertical red bars with an X were not recovered as monophyletic in that analysis. Faded colour bars represent that the clade was included but relationships alternated. P indicates paraphyletic lineages. Clades without an X or bar were supported; the lack of a bar indicates the clade was supported but the deeper relationships were not. Higher group names refer to the classification before Burks et al. (2022). Family abbreviations expanded in Table S1.Published as part of <i>Cruaud, Astrid, Rasplus, Jean-Yves, Zha, Junxia, Burks, Roger, Delvare, Ǵerard, Fusu, Lucian, Gumovsky, Alex, Huber, John T., Jan̆sta, Petr, Mitroiu, Mircea-Dan, Noyes, John S., Noort, Simon van, Baker, Austin, Bohmova, Julie, Baur, Hannes, Blaimer, Bonnie B., Brady, Sean G., Bubeńıkova, Kristyna, Chartois, Marguerite, Copeland, Robert S., Papilloud, Natalie Dale-Skey, Molin, Ana Dal, Dominguez, Chrysalyn, Gebiola, Marco, Guerrieri, Emilio, Kresslein, Robert L., Krogmann, Lars, Lemmon, Emily, Murray, Elizabeth A., Nidelet, Sabine & Nieves-Aldrey, Jośe Luis, 2023, The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps, pp. 1-30 in Cladistics 2023</i> on page 9, DOI: 10.1111/cla.12561, <a href="http://zenodo.org/record/10115140">http://zenodo.org/record/10115140</a&gt