“mutant populations” page, mutants can be
browsed by sample name, trait, image, and
phenotype.
23.3.2Medicago truncatula
The Medicago HAPMAP project (http://www.
medicagohapmap.org) was spearheaded by an
internal consortium. The project involves rese-
quencing 384 inbred lines ofM. truncatulawith
the purpose of discovering single-nucleotide
polymorphisms (SNPs), insertions/deletions
(INDELs), and copy number variants (CNVs).
This information is useful for describing the
population structure, identifying genome seg-
ments, and genome-wide association (GWA)
mapping. The 338 germplasms can be ordered by
users of the database. The genome structure of
Mt3.5 and Mt3.0 can be browsed by GBrowse.
The SNP data of Mt4.0, Mt3.5 and Mt3.0 can be
obtained from the download page. The updated
M. truncatulagenome information is currently
available from J. Craig Venter Institute (http://
jcvi.org/medicago/).
23.3.3Lotus japonicus
23.3.3.1 Miyakogusa.jp
Miyakogusa.jp (http://www.kazusa.or.jp/lotus/)
was established in 2008 to facilitate publication
ofL. japonicus genomic information. The top
page of the database is shown in Fig.23.1. The
page is divided intofive sections: (1) Menus, (2)
Links, (3) News, (4) Keyword search for the
predicted genes, and (5) Genome browser. At the
time of writing, the website is based on version 2.
5 of the genome. An earlier release of the Lotus
genome, version 1.0, is also available. The
database and website will be updated to version
3.0 on its release. The database contains links to
the related databases, such as“Legume Base”at
Miyazaki University (http://www.legumebase.
brc.miyazaki-u.ac.jp) and “Worldwide Lotus
Science Information Desk” at the National
BioResource Project (NBRP) (http://www.
shigen.nig.ac.jp/infodesk/topSpeciesAction.do?
speciesId=4). Users can access the information
related toMesorhizobium loti, the symbiont ofL.
japonicus, released from Rhizobase (http://
genome.microbedb.jp/rhizobase/Mesorhizobium/
), expression sequence tags (ESTs) sequenced by
Kazusa DNA Research Institute (KDRI) (http://
est.kazusa.or.jp/en/plant/lotus/EST/), transcript
sequences released from“The Gene Index Pro-
jects”performed by Harvard University (http://
compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.
pl?gudb=l_japonicus), and the chloroplast gen-
ome sequence obtained by KDRI (http://www.
kazusa.or.jp/lotus/Cp/). The menus on the top
page are comprised of“Clone list,”“Genetic
map,”“Insertion tag lines,”“BLAST,”“Data-
base download,” and “LjMG RI lines.” The
contents in each menu are shown as follows.Clone List
The clones used for genome sequencing were
anchored by genetic markers and physical linkage
information, and comprised six linkage groups
(chromosomes 1–6) and unanchored clones. The
linkage maps can be browsed on the top page of
“Clone list”as shown in Fig.23.2. Users canfind
the clone from the list shown on the page or by
using the search function to search by clone name.
In the list, the assembly phase and sequence
redundancy of each clone are also listed. In the
version 2.5, 291 (SSR: 270, dCAPS: 21), 201
(SSR: 187, dCAPS: 14), 204 (SSR: 192, dCAPS:
12), 186 (SSR: 169, dCAPS: 17), 167 (SSR: 154,
dCAPS: 13), and 106 (SSR: 101, dCAPS: 5)
markers are located on 95, 63, 72, 58, 61, 44
contigs consisting of 540, 363, 370, 383, 321, 210
clones from chromosomes 1–6, respectively. The
174 clones on 9 contigs are not integrated into the
linkage groups and are collected as unmapped
clones. By clicking the marker name, users can
access marker category information (SSR or
dCAPS), primer sequences (Fw/Rv), EST or
genome sequences, PIC values, position of
markers on linkage map (Miyakojima MG-
20 ×Gifu B129), single-nucleotide polymor-
phisms (SNPs), simple sequence repeats (SSRs)23 Legume andLotus japonicusDatabases 261