Blanc SVSE 6 - Blanc - SVSE 6 - Génomique, génétique, bioinformatique et biologie systémique

MicroRNAs and phenotypic plasticity – MiRNAdapt

For an organism to adapt to its environment, communication between its genes is required, forming a network.

A living organism is submitted regularly to changes of its local environment, such as seasons. An organism needs to adapt in order to survive, and this involves complex interactions between the products of the thousand of genes, such as the messenger RNAs or the microRNAs.

Aphids are able to change the functioning of their genes to adapt to seasons.

The aim is to better understand the biology of aphids (that are pests) in order to fight them more efficiently. Herein, we propose to describe the networks of genes involved in adaptation of aphids to seasons. The 34.000 genes of an aphid genome (the pea aphid for this study) are not active all together when seasons alternate. Some are activated, other are repressed. This allows aphids to alternate their reproductive mode between a clonal viviparous reproduction in spring and summer and a sexual oviparous reproduction in autumn. We thus want to describe and understand how the activity of the genes that are required for this transition and adaptation is affected by seasons. This means analysis thousand of possible interactions between messenger RNAs and their regulators miRNAs. This can be performed thanks to recent breakthroughs in genome analyses, the so-called genomics.

Biology entered for more than a decade into the era of genome analyses, such as the genome of the pea aphid, the model species of this project. Thanks to these genomic resources, we can now describe the active genes producing messenger RNAs or microRNAs when aphids adapt to the seasons. We will thus analysed the interactions between all these molecules (more than 30.000 messenger RNAs and several hundreds of miRNAs). For this, we couple techniques developed by informatics adapted to biology (bioinformatics) as well as mathematical modeling to predict interactions.

This research will enrich our knowledge of the functioning of aphid genomes, pests of many crops. This project will also produce new methods to create and analyse networks of interactions between genes, applicable to many other living organisms.

The knowledge produced by this project will identify key functions of the aphid pests, on which tools to limit their infestation could be specifically developed in the future. Reducing by 50% pesticide usage is part of the French Ecophyto 2018 initiative, in a context where protecting the environment is a key demand.

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Understanding how genes and the environment interact to shape phenotypes is of fundamental importance for resolving important issues in adaptive evolution. Yet, for most model species with mature genetic and accessible genomic resources, we know little about the natural environmental factors that shape their evolution. By contrast, animal species with deeply understood ecologies and well characterized responses to environmental cues are rarely subjects of genomic investigations. The context of this project takes place in advances in genomics in aphids transforming research on the regulatory mechanisms of phenotypic plasticity. Aphids are pests to plants and have the capacity to produce extremely divergent phenotypes in response to environmental stimuli. Sexual fate and reproductive mode are condition-dependent in aphids which are capable of alternating morphology, physiology and behavior in response to abiotic cues. Recently the genome sequence for the pea aphid Acyrthosiphon pisum was described. We propose here an integrative study between bioinformatics, genomics and mathematical modeling focused on the transcriptional basis of the plasticity of the reproduction mode in response to the modification of environment. This approach will provide broad insight into adaptive plasticity and genome by environment interactions.
The consortium proposes complementary expertises that will allow i) the identification of the putative interactions between the whole set of miRNAs and mRNAs of the pea aphid, ii) the construction of a network based on these putative interactions, iii) the identification from this network of the nodes centered on the miRNAs known to be regulated by the reproductive mode, and iv) the validation by bench experiments of the main hypotheses of the network by a looping scenario with modeling. The first scientific Task will predict miRNA:mRNA interactions in the pea aphid, based on sequence conservation between insect genomes of their predicted miRNAs and their predicted 3’UTR regions of the transcripts. The second scientific task will construct a network of regulation involving miRNAs and their predicted mRNA targets, centred on the miRNAs and mRNAs known to be regulated during phenotypic plasticity of the reproductive mode. Before this, Task 2 will identify putative transcription factor binding sites common to co-regulated genes during sexual or asexual embryogenesis, respectively. The third and last task will validate (or not) part of the network by re-sequencing miRNAs from variants of the pea aphid that have lost the capacity to switch reproductive modes, and by knock-down of a couple of miRNAs at key nodes of the network.For this, the consortium proposes complementary expertises that will allow i) the identification of the putative interactions between the whole set of miRNAs and mRNAs of the pea aphid, ii) the construction of a network based on these putative interactions, iii) the identification from this network of the nodes centred on the miRNAs known to be regulated by the reproductive mode, and iv) the validation by bench experiments of the main hypotheses of the network. The first scientific Task will predict miRNA:mRNA interactions in the pea aphid, based on sequence conservation between insect genomes of their predicted miRNAs and their predicted 3’UTR regions of the transcripts. The second scientific task will construct a network of regulation involving miRNAs and their predicted mRNA targets, centred on the miRNAs and mRNAs known to be regulated during phenotypic plasticity of the reproductive mode. Before this, Task 2 will identify putative transcription factor binding sites common to co-regulated genes during sexual or asexual embryogenesis, respectively. The third and last task will validate (or not) part of the network by re-sequencing miRNAs from variants of the pea aphid that have lost the capacity to switch reproductive modes, and by knock-down of a couple of miRNAs at key nodes of the network.

Project coordination

Denis TAGU (INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE RENNES) – denis.tagu@rennes.inra.fr

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

CNRS CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - DELEGATION REGIONALE BRETAGNE ET PAYS- DE-LA-LOIRE
IGH (UPR 1142 CNRS) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - DELEGATION REGIONALE LANGUEDOC-ROUSSILLON
UMR BiO3P INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE RENNES

Help of the ANR 226,000 euros
Beginning and duration of the scientific project: February 2012 - 36 Months

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