et al. 2012 ). The resource was subsequently
expanded and redesigned into a general L.
japonicusgenomics resource known as Lotus
Base.
All resources available through Lotus Base
are based onL. japonicusgenome version 2.5,
with version 3.0 release pending in the near
future.
LORE1 Database and Line Ordering
At the time of writing, the database contained
96,905 LORE1 insertions registered in 32,272
unique plant lines (300001–30057983). Each
insertion is tagged with a unique BLAST header
containing the chromosome number, chromo-
somal position, and insertion orientation, allow-
ing these insertions to be accessible from BLAST
searches against the LORE1 insertions database.
Users can retrieve plant lines of interest from the
search page (http://users-mb.au.dk/pmgrp/
lore1search.php) based on user-defined criteria:
BLAST header, plant line/ID, chromosome,
chromosomal position, and gene name or anno-
tation, or a combination thereof (Fig.23.6). The
search results will return appropriate plant lines,
each complete with information cross-referenced
from database tables including gene name,
annotation, forward and reverse genotyping
primers, expected PCR fragment sizes of wild
type and insertional mutants, and the ±1kb
flanking sequence surrounding the LORE1
insertion site. The search form is accessible via
“LORE1[LORE1 lines seach”[Fig.23.5(1)].
From the results page, users are able to further
refine their search based on alternative plant line
(s) or gene(s) of interest, and access geneFig. 23.5 Landing page ofLotusBase (http://carb.au.dk/
lotus-base/). The main tools useful to the end users are
grouped under navigation categories: (1)“LORE1”con-
tains resources pertaining to LORE1 insertional muta-
genesis lines, such as LORE1 line search, line order status
and order form; (2)“Tools”is a collection of usability
tools designed for the resource, including an in-house
modified version of NCBI wwwblast suite; (3)“Resour-
ces”contains downloadable manuals, scripts and pro-
grams related to the project; and (4)“Info”hosts a
repertoire of commonly asked questions on the use,
application, genotyping and general information of
LORE1 lines, and usability tools23 Legume andLotus japonicusDatabases 265