The Lotus japonicus Genome

(fragment size, motif pattern, number of motif
repeat), gel images, and enzyme-related markers.

Genetic Map
The location of contigs ordered by markers on
each chromosome can be browsed at the top of
the “Genetic map” page shown in Fig. 23.3.
Users can access the marker list consisting of
marker names, linkage groups, and genetic
positions. The page also has clickable maps for
each chromosome. As shown in Fig.23.4, the
detailed information on markers described in the
“Clone list”section is displayed at the right side
of the linkage map.

Insertion Tag Lines
The gene-tagging populations were established
by using an endogenous long-terminal repeat
(LTR) retrotransposon, Lotus Retrotransposon 1
(LORE1), in Denmark and Japan. The list of
LORE1 tag lines of 32,272 (300001–30057983)
and 1,227 (P001–P2550), established in Den-
mark and Japan, respectively (Fukai et al. 2012 ;
Urbanski et al. 2012 ), is available on the top page
of“Insertion tag lines”(http://www.kazusa.or.jp/
lotus/LORE1/). In each plant line, the inserted

positions related to genes and functions predicted

by homology searches against TrEMBL (http://

http://www.ebi.ac.uk/uniprot) were summarized.

Through this page (example for plant line P0001:

http://www.kazusa.or.jp/lotus/predict/cgi-bin/

LORE1_lineinfo.cgi?id=P0001), users can

order plant lines from Legume Base devel-

oped by National BioResource Project

(NBRP). Users can search the query sequence

against LORE1 insertion sites by using

BLASTN (Altschul et al. 1997 )onthetop

page of“Insertion tag lines.”

BLAST Search

On the BLAST search page (http://www.kazusa.

or.jp/lotus/blast.html), users can perform sear-

ches against all predicted genes and clones

(contigs) of versions 2.5 and 1.0, and also against

LORE1 insertion sites. This page was based on

the Web BLAST interface distributed at NCBI

(http://www.ncbi.nlm.nih.gov).

Data Download

The genome contigs and pseudomolecules, gene,

and protein sequences can be downloaded from

this page, and gene model and assembly were

Fig. 23.1 Top page of miyakogusa.jp. Users can browse the contents from (1) Menus, (2) Links, (3) News, (4)
Keyword search, (5) Genome browser

262 H. Hirakawa et al.