To investigate the whole genetic system of legume species, we have been analyzing the genome of a model legume, Lotus japonicus. The latest version of the genome sequence information (release 2.5) generated by clone-by-clone and selected TAC mixture sequencing is provided through our web database, “miyakogusa.jp” (http://kazusa.or.jp/lotus/). Toward the completion of L. japonicus genome sequencing, we are currently working on further improvement by adding the sequence information generated from second generation sequencers. By integrating paired end sequences generated from 454 and Illumina sequencers, scaffolding and gap filling of current pseudomolecules are on going. Status of this integration approach will be presented. Along with the accumulation of genome information, the demand for an efficient experimental tool for gene function analysis has been increasing. Reverse genetics is one of the effective approaches. In order to establish the basis for reverse genetic approach, we are currently preparing large scale insertion tag lines applying endogenous retrotransposon of L. japonicus named LORE1. Since LORE1 transposition occurs in the germline, seeds harvested from a single activated line have different insertion sites in their genomes, and thus can be considered as independent tag lines. The large-scale detection of LORE1 insertion sites using second generation sequencers revealed a preference for genic regions, especially in exons of protein coding genes. With these features suitable for gene tagging line construction combined with established high-throughput FST analysis system, LORE1 insertion lines pave the way to development of a comprehensive reverse genetic resource.