Organisms across the tree of life are associated with diverse microbial partners that impact host adaptive traits and exhibit phenotypes ranging from parasitism to mutualism. For example, insects thriving on nutritionally unbalanced habitats are prone to house mutualistic intracellular bacteria (endosymbionts) that complement their diet, thus greatly improving their ecological performances. Within insects, endosymbiosis is very common in the Curculionoidea weevils superfamily, which constitutes a group with considerable worldwide biodiversity. Weevils include some of the most invasive insects and cause huge crop damages. Recent phylogenetic and molecular studies have shown that endosymbiosis history has been marked by several symbiotic displacements within this insect group. The most recent event may have occurred less than one million year ago within the cereal weevil Sitophilus clade resulting in the replacement of an ancestral symbiont Candidatus Nardonella by Sodalis pierantonius symbiont. S. pierantonius genome exhibits peculiar molecular features associated with a massive pseudogenization and the occurrence of a huge amount of repeated elements. Whether these phenomena are adaptive, and whether they impact host genome reshaping are puzzling questions that will be addressed thanks to the genome level investigation of the Sitophilus-Sodalis recent association. Here, we present the draft genome sequence of the rice weevil Sitophilus oryzae. The full genome sequence has been obtained through a combination of short-read (Illumina HiSeq and Roche/454 GS FLX) and long-read (Pacific Biosciences PacBio RS) sequencing methods. After error correction, the data were assembled using the Platanus algorithm for an initial scaffolding and gap-filling. These scaffolds were then re-scaffolded several times using PacBio data. The final assembly consisted in 17,365 scaffolds of a total length of 652 Mbp (the S. oryzae genome size was estimated to be about 650 Mbp using flow cytometry), a N50 value of 110 kbp, a coverage of 101X and a GC content of 38.4%. Intriguingly, transposable elements (TE) analysis using both automated tools (dnaPipeTE, RepeatModeler and MITEhunter) and manual annotations revealed an unexpected high amount of repeated DNA (>50%) in this weevil genome. Gene prediction was then performed using a combination of MAKER, GeneMark, Augustus and SNAP algorithms and taking advantage of the available transcriptomic data (EST and RNA-seq data) on S. oryzae to build more accurate gene models. Finally, the official gene set contained 17,026 protein-coding genes. Based on this gene set, the complete catalogue of gene phylogenies (phylome) was predicted through the PhylomeDB pipeline and will be publicly available in this database (www.phylomedb.org). The weevil metabolic and signalling networks were also reconstructed using the CycADS pipeline in order to generate the SitorCyc database (a BioCyc interface of the S. oryzae metabolism). These metabolic pathways were integrated in the ArthropodaCyc database collection dedicated to comparative metabolic analyses among arthropods (http://arthropodacyc.cycadsys.org/). The interdependence of the metabolic networks of S. oryzae and its endosymbiont S. pierantonius will then be characterized thanks to their integration into the ArtSymbioCyc database that is being developed and will be dedicated to arthropod symbioses. All these annotations (TE, phylome and metabolic networks) will be integrated in a comprehensive genome database providing a genome browser with crosslinks to available resources. Altogether, these results are expected to unravel basic molecular mechanisms and evolutionary features associated with the establishment and the maintenance of endosymbiosis in animals, and to permit identifying potential gene targets useful for the development of new ecologically-friendly strategies for pest insects control and management.