Fabaceae is the third largest family of flowering plants, comprising 650 genera and 18 000 species with a variety of characteristics; many of which have long been targets of breeding because of their agronomic and industrial importance. Among them, a few species have been chosen as ‘model legumes’ for use in genetic and physiological studies. Lotus japonicus
is a typical model legume with the characteristics of a short life cycle (2–3 months), self-fertility, and a relatively simple genome architecture of diploidy (n
= 6), i.e. small in size, 472 Mb. Mutants in various biological phenomena specific to legumes such as symbiotic nitrogen fixation, and those common to flowering plants such as flower morphogenesis, have been characterized and the genes responsible have been isolated and further studied. The availability of the Agrobacterium
-mediated DNA transformation system and genomic resources including a large number of expressed sequences tag (EST)/cDNA clones,1
high-density genetic linkage maps,2–4
and partial genome sequences5–9
has played an essential role in this process.
The whole-genome sequences of two plant species, Arabidopsis thaliana (Cruciferae) and Oryza sativa (Poaceae), have drastically accelerated research into their genetic systems by providing investigators with both gene sequences and positional information. However, the process of high-accuracy sequencing is expensive and labor intensive since physical maps are created and a large number of individual BAC clones are used as templates. In contrast, draft sequencing according to the whole-genome shotgun approach in combination with BAC end sequencing generates information about the general genome structure at a fairly reasonable cost, but the resulting data are rather fragmentary and need an additional effort to be connected with physical/genetic maps. In this study, we aimed to analyze the genome structure of L. japonicus to reveal gene and genome features that are characteristic of legume plants. For this purpose, we adopted various established technologies including genomic library construction, DNA sequencing, fluorescent in situ hybridization (FISH), genetic mapping and bioinformatics in such a way that the advantages of each technology were combined in a cost-effective manner. Here, we report the first whole-genome structure of the legume, L. japonicus, its characteristic genome features, and a variety of information and material resources that were developed during this study.