Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.

crops such as corn, sorghum and soybean. While FAW larvae are considered polyphagous, differences in diet preference have been described between two genetic variants: the Corn strain (sf-C) and the Rice strain (sf-R). These two strains are sometimes considered as distinct species, raising the hypothesis that host plant specialization might have driven their divergence. Ecological speciation takes place when adaptations to different ecological niches lead to the reproductive isolation of two populations. Under this hypothesis, we expect that the transcriptional response to the host plants should affect differently the fitness of the two FAW strains. We also expect that these genes should also be linked to a reproductive isolation mechanism between the strains. In this study, we performed controlled reciprocal transplant (RT) experiments to address the impact of plant diet on several traits linked to the fitness of the sf-C and sf-R strains. The phenotypical data suggest that sf-C is specialized to corn. We then used RNA-Seq to analyze the gene expression of FAW larvae from RT experiments. We show that each strain has a different response to the same plant diets. However, we also found constitutive transcriptional differences between strains in laboratory and in natural populations. In particular, we show that mitochondrial transcription is the main difference between strains. A difference in mitochondrial function may be the basis for a shift in host plant and could be involved in hybrid incompatibility, raising the hypothesis that mitochondrial genome is the main target of selection between the two strains.. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. (Goergen et al. 2016;Jeger et al. 2017).The FAW is a polyphagous species, being documented on over 100 plants from 27 different families (Pogue 2002). However, using allozymes electrophoresis monitoring, a significant genetic heterogeneity has been observed in FAW . CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/263186 doi: bioRxiv preprint first posted online Mar. 5, 2018; 4 populations that was associated with feeding preferences (Pashley et al. 1985;Pashley 1986). One genetic haplotype was mostly found on corn (Zea mais), sorghum (Sorghum spp.) and cotton (Gossypium spp.) and was named the corn strain (sf-C). Another haplotype was found associated to individuals collected on smaller grasses such as turf, pasture (Cynodon dactylon) grasses and rice (Oryza spp.), and has been named the rice strain (sf-R) (Pashley 1988). Subsequent studies have confirmed these genetic differences on markers such as the mitochondrial gene Pashley and Martin 1987;Pashley, Hammond, and Hardy 1992). In order to detect post-zygotic...

A naplasmoses are emerging tickborne zoonoses caused by intracellular bacteria of the Anaplasma genus. In total, 8 Anaplasma species and several candidate species have been described, including at least 5 species infecting humans (1,2). Of particular concern, the agent of human granulocytic anaplasmosis, A. phagocytophilum, has a specific tropism to polymorphonuclear neutrophils (1,3). Another species, provisionally named A. capra, recently described from asymptomatic goats, is now recognized as an agent of human intraerythrocytic anaplasmosis in China (4). The 3 other species detected in humans are major veterinary agents sporadically identified in few patients worldwide: A. ovis and A. bovis in erythrocytes and A. platys in platelets (1,5). Human anaplasmosis are consistently associated with persons who live in rural areas in habitats favorable to ticks or who work closely with domestic animals (1,6). However, recent surveys report the presence of novel Anaplasma species of undetermined zoonotic potential in wild fauna (1,2). The StudyWe assessed the presence of Anaplasma in blood samples of clandestine gold miners working in the Amazon rainforest of French Guiana. This 83,000 km 2 territory, located between Suriname and Brazil, is one of the regions of highest biodiversity in the world, with >280 species of wild mammals (7). The human population of French Guiana (≈284,000 inhabitants) is concentrated principally in a handful of towns spread along the coastline and the 2 main rivers (8). The interior is largely uninhabited and covered by dense rainforest, where illegal gold mining camps are located (9,10).We examined 363 archived DNA extracts obtained from human blood samples. We primarily collected these samples in 2019 as part of Malakit, a malaria survey in remote mining camps in French Guiana (11). To characterize the whole bacterial diversity, we typed DNA blood samples by using a high-throughput bacterial 16S rDNA (rrs) sequencing approach (bacterial barcoding) (12). Bacteria were characterized as operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) and taxonomically assigned by using the Silva database (https://www.arb-silva.de).Examination of OTUs and ASVs revealed the presence of Anaplasma sequences in 1 DNA sample.No OTU or ASV assigned to the Anaplasma genus or to the Anaplasmataceae family was detected in the 362 other samples. We further conducted 2 independent Anaplasma-specific PCRs targeting a region of the 16S rDNA gene (544 bp) and the 23S-5S (ITS2) intergenic region (423 bp) using techniques described by Calchi et al. (13) and obtained amplicons of correct sizes for the positive sample. The Sanger sequencing of amplicons obtained with each pair of primers