Genome structure of the legume, Lotus japonicus

Abstract

The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10,951 complete and 19,848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes.

Figure 1

FISH detection and the integration map of L. japonicus. (A and C) Mitotic prometaphase chromosomes and meiotic pachytene chromosomes were stained with DAPI. (B) TAC clone, LjT30P03 (corresponding marker: TM0148) (green, arrowhead) was detected on the long arm of chromosome 5. 45S rDNA (red) was detected on the short arms of chromosomes 2, 5, and 6. (D) LjT30P03 (corresponding marker: TM0148) (green, arrowhead) was detected on chromosome 5 of the pachytene chromosome. The error bar represents 5 μm. (E) Integration among three maps; mitotic prometaphase chromosome map, meiotic pachytene chromosome map, linkage map of L. japonicus. Red circles show TAC clones, yellow and orange show ribosomal RNA genes, green shows tandem repeat LjTR1, blue shows retrotransposon LjRE2 representing the centromere. The length ratio among six chromosomes was adjusted to the ratio of pachytene chromosomes.

Figure 2

Plant GOslim category classifications. The results of functional categorization are shown for 10 representative GOslim classes of ‘Molecular function’ (A) and ‘Biological process’ (B). GO was automatically annotated on the L. japonicus protein-encoding genes by searching InterPro domains.

Figure 3

Segmentally duplicated regions in the L. japonicus genome. Individual chromosomes are depicted as horizontal bars. Colored boxes with the same color code connected by the blue line indicate each pair of duplicated segments. Duplicated segments in reversed orientation are connected with dotted lines. The scale is in megabases.