While a global food crisis threatens, 20 % of crops are eaten by insects. Providing knowledge on insect pest genomes, and on the ability of insects to adapt to different host-plants and to diversify may help deciphering new crop plant protection strategies. One such pest is the Lepidoptera Spodoptera frugiperda, the fall armyworm (FAW). It exists as two different host-plant strains, one mostly associated to corn (C strain) whereas the other is mostly associated to rice (R strain). The two strains are morphologically indistinguishable but they exhibit pheromone and behavioral differences, and some degree of genetic incompatibility. The first aim of the project is to record all sources of genetic variation between the two strains by comparing the whole genomes of both lab strains, but also by measuring levels of host-based genetic divergence and of genes flow between field individuals on different host-plants. The second aim of the project is to identify genes involved in adaptation to the host-plant and their regulation, and to determine if adaptation to the host-plant has a role in speciation. We will start the project from the already available full genome assembly and genes annotation of the C strain genome(from Genoscope), and the whole genome assembly of the R strain (from one/two laboratory individuals in each case) as well as from transcriptomic data of both strains and of a 300 microsatellites markers based genetic map. The project will include: - A complete structural annotation of both laboratory strains recording all orthologs, and mutations (SNP, rearrangements, TE insertions) that make heterogeneity between the two genomes. Candidate genes under divergent selection or under the direct influence of positive selection will be listed. - A functional annotation of the two genomes. It will be performed by comparing transcriptomes (mRNAs and small ncRNAs) of the two strains on two host-plants at larval and adult stages. Genes with modulated expression will be identified and their epigenetic regulators (histones modifications and small ncRNAs) will be analyzed on the same samples. Analysis of these data will rely on bioinformatic data integration effort. - A set of 50 genes chosen among divergent and differentially expressed genes will be further analyzed. We will focus on gene families possibly involved in host-plant adaptation. We will check on field individuals if the modulated expression variation is found also associated to the host-plant, or if divergent alleles are enriched in natural populations on the cognate host-plants. We will also follow the expression level and sequence of these genes in laboratory individuals upon 12 successive host-plant choice trials in order to check whether they are subject to microevolution. - A measurement of host-based genetic divergence and genes flow between individuals on different host-plants at a local scale. We will perform a phylogeographic analysis in order to describe population structure and measure strain divergence at a regional scale. The consortium includes four partners. The DGIMI’s coordinator lab is expert in genomics, transcriptomics and epigenomics of insects. The URGI lab is expert in de novo detection of Transposable Elements (TE) in genomes and their classification, Symbiose lab is expert in bioinformatic treatment and analysis of genomic and post-genomic data, whereas CBGP lab is expert in population genetics and phylogeography of insects. . None of the partner would have been able to conduct such a project alone, and the complementary expertises in genomics, genetics, evolution and bio-informatics will constitute a major strength for this joint scientific innovative