La PF Transcriptome et Epigenome développe des projets de séquençage à haut débit (collaboration et service) avec des équipes du Campus. Ceux-ci couvrent l'ensemble des thématiques du campus ainsi qu'une large gamme d'organismes (des virus aux mammifères). La plate-forme exerce des activités de biologie humide (construction des librairies et séquençage) et de biologie sèche (analyse bioinformatiques et statistiques). La personne mise a disposition interagira étroitement avec les autres bioinformaticiens du pôle BioMics et du Hub. Ses activités concerneront notamment: - La participation à la conception et à la mise en place des projets avec les équipes demandeuses, la prise en charge des analyses et le reporting aux utilisateurs - La mise en place d'un workflow d'analyse bioinformatique des données de transcriptome /épigénome en étroite collaboration avec le C3BI, la DSI et les autres bioinformaticiens du pole. Ce workflow permettra le contrôle qualité des données, leur prétraitement, le mapping des séquences sur les génomes/transcriptomes de réference, et le comptage des reads pour les différents éléments de l'annotation - L'adaptation du workflow d'analyse aux questions biologiques et aux organismes étudiés dans le cadre des activités de la PF - L'activité de veille technologique et bibliographique (test et validation de nouveaux outils d'analyse, updates d'outils existants...) - La mise en place et le développement d'outils d'analyse adaptés aux futurs projets de la PF: single cell RNAseq, métatranscriptome, ChIPseq, analyse des isoformes de splicing.. Ceci se fera notamment via la réalisation d'analyses dédiées avec certains utilisateurs. Les outils mis en place et validés dans ce cadre seront ensuite utilisés pour l'ensemble des projets. - L'activité de communication et de formation (participation aux réunions du consortium France Génomique,formation permanente à l' Institut Pasteur… - la participation a d autres projets du Pole BioMics (selon disponibilité) Bernd Jagla, qui était le bioinformaticien de la plateforme a rejoint le Hub au 1er janvier 2016. Rachel Legendre est mise a disposition depuis le 2 novembre 2015 et remplace Bernd Jagla. Je souhaite que Rachel Legendre soit mise à disposition de la plateforme pour une durée d'au moins 2 ans.

We are comparing the bacterial communities of domestic and sylvatic  breeding sites and midguts of Aedes aegypti collected in Gabon.

Insect vectors durably transmit many important human and animal diseases. Insects are mobile, adaptable and difficult to control, which makes them efficient vehicles for disease emergence, spread and maintenance. Genomic tools have been applied to the study of vectors and vector control, and some insects such as the African malaria vector Anopheles gambiae have now become new model organisms for natural host-pathogen interactions. We study mosquito vectors of malaria and arboviruses, which generates four main kinds of large-scale data that requires dedicated bioinformatics expertise: i) functional dissection of mosquito immune signaling pathways by RNAseq transcriptome profiling to detect responses to pathogen infection and/or silencing of target genes, including mRNA as well as small and other non-coding RNAs, ii) next-gen genetic linkage mapping by deep sequencing of index-tagged phenotyped individual mosquitoes, iii) population genomic analysis by whole-genome sequencing of hundreds of individual 250Mb mosquito genomes, iv) metagenomic analysis of the mosquito microbiome and pathogen susceptibility, and of ecological metagenomic communities in field samples of mosquito vectors.

Anopheles mosquitoes are the vectors of Plasmodium parasites, the etiological agents of malaria in humans. In Anopheles gambiae, a major vector in Africa, parasite transmission is largely under genetic control. We have previously shown that a gene family is implicated in the immune control of the parasite in this vector. The response of the family members is pathogen-specific, with one controlling P. falciparum infection and the other controlling rodent parasites. Recently, the genome of Anopheles stephensi, the major Asian vector, has been sequenced and, in this species, there is only one gene. Knocking down this gene reduced lifespan of A. stephensi and antibiotic treatment restores a normal longevity, suggesting the implication of the gut microbiota. Therefore, we conducted a metagenomic analysis in order to identify the bacteria responsible for the shorten of the mosquito lifespan.

The genome of the yellow fever mosquito (Aedes Aegypti) is not fully annoyed, and this project aims at discovering novel transcripts using RNAseq data.

The goal of the project is to determine if there are differences in the midgut microbiome of our lab colonies of Aedes aegypti. We frequently observe various phenotypic differences between different colonies of mosquitoes and it is a recurring question whether these phenotypic differences are a result of differences in the microbiome. We will sequence the microbiome of 6 representative established lab colonies that have been collected from geographically diverse areas and compare the bacterial communities between the them. This data will help us dissect the importance that variation of the midgut microbiome of lab colonies of Aedes aegypti has on the phenotypic differences we observe in the lab.

Yellow fever virus (YFV), a Flavivirus transmitted by mosquitoes causes a severe hemorrhagic fever in humans. Despite the availability of a safe and effective vaccine (17D), YFV is still a public health problem in tropical Africa and South America. In the Americas, the massive campaign of mosquito control during the first half of the 20th century led to the eradication of Aedes aegypti from most American countries, and as a consequence, urban outbreaks of YF were no longer observed. However, the relaxation of vector control led to the reinfestation of urban areas by Ae. aegypti and the subsequent establishment of the Asian tiger mosquito Aedes albopictus. In Brazil, while human cases are sporadically detected in the Amazonian basin where sylvatic YFV strains circulate between non-human primates and arboreal canopy-dwelling mosquitoes (Haemagogus sp.), they are increasingly reported outside the jungle moving towards the Atlantic coast, the most populated area. In the absence of routine immunization programs, YF may come back in the American towns as it was in the past. The causes leading to the current YF resurgence are multifactorial. From a mosquito vector viewpoint, changes in vector densities, distribution, vector competence or vector as a site of selection for epidemic YFV strains, can be regarded as critical factors. Our project aims to address the contribution of the invasive mosquito Ae. albopictus as a missing link to allow a selvatic YF strain (1D) to become adapted for a transmission in urban areas by the human-biting mosquito, Ae. aegypti. It will be done through three specific objectives: (i) identify Ae. albopictus-adaptive mutations after serial cycling of the selvatic YFV-1D on Brazilian Ae. albopictus mosquitoes, (ii) evaluate their potential to be transmitted to a vertebrate host, and (iii) deepen the transmission of the experimentally selected viruses by field-collected mosquito populations.

In early development, regulation of transcription results in precisely positioned and highly reproducible expression patterns that specify cellular identities. How transcription, a fundamentally noisy

Aedes albopictus is an important vector for transmitting arboviruses, such as Dengue, Chikungunya, West Nile or Zika viruses. Its worldwide distribution due to its high ability to adapt to variable en

As a result of combined climate change and globalization (increased flow of travelers and goods), the distribution of the mosquito Aedes albopictus is expanding significantly outside tropical regions.

Despite the worldwide importance of malaria due to Plasmodium vivax, there is currently almost no data on the molecular responses of the Anopheles mosquito vectors to this parasite species. Understa

This project to characterize defective viral genomes of shrimp pathogens i.e. Yellow head virus (YHV) from next-generation sequencing of viral RNAs data by using DI-tector or similar tools. NGS data

Although the microbiota of mosquitoes is known to play an important role in their vectorial capacity for human pathogens, most earlier studies have focused on mosquito-bacteria interactions at the adu

Our research team recently identified an Aedes aegypti mosquito population that is partially resistant to dengue virus infection. We also have candidate genes that potentially innerly this phenotype.

Lyme borreliosis (LB) is an important tick-borne disease which can cause a broad range of symptoms mainly affecting the skin, the nervous system and the joints. It is caused by bacteria of the Borreli

Cepia mass produces two species of Anopheles mosquitoes for research teams studying malaria. The aim of this project is to assess 1) whether or not the compostion of the bacterial microbiota fluctuate

We are currently characterising a set of genes that are involved in the yellow fever mosquito, Aedes aegypti, vector competence. We would like to investigate the polymorphisms of those genes using ex

The mechanisms underlying Anopheles mosquito susceptibility to malaria parasite infection in nature are not understood. We infected wild Anopheles pedigrees in West Africa to map loci for susceptibili

The highest global malaria prevalence is in Africa, where the most important vectors are members of the Anopheles gambiae species complex. We generated a large curated panel of infected wild Anopheles

Enhancers are cis-regulatory elements that control developmental and spatial gene expression in eukaryotes. Enhancers have been little studied in mosquitoes, including the Anopheles vectors of malaria

Investigating the genetic basis of an organism’s phenotype typically focuses on genomic sequences annotated as genes. This traditional approach ignores repeated sequences such as transposable elements

This projects aims at performing transcriptomics on mosquitoes infected with arboviruses such as Dengue or Zika virus.

To better understand the vector specificity of Aedes aegypti mosquito in the transmission of CHIK virus, we try to identify genes involved in the primary responses of the viral infection when the viru

Describing viruses of invertebrate vectors of disease, provides better understanding of evolution and host range for various virus groups. In addition to filling the gaps in the current knowledge of t

Before the WHO considered it as a public health emergency of international concern in February 2016, Zika virus (ZIKV, Flavivirus, Flaviviridae) was a neglected mosquito-borne virus. First identified

To better understand the vector specificity of Aedes aegypti mosquito in the transmission of the alphaviruses CHIKV and ONNV, we are using an in vitro system to specifically depict critical viral infe