Sequenced Insert Populations

1

• Sequenced Insert Populations
•  
• Several large populations of Arabidopsis lines
  have been mutated by transposon derived elements
  and the DNA sequences adjacent to the insertion
  sites have been sequenced. These populations
  include
• SLAT lines (Prof Jonathan Jones - John Innes
  Centre)
• IMA lines (Prof Venkatesan Sundaresan -
  Institute Molecular Agrobiology)
• ITS lines (Dr Andy Pereira - CPRO)
• CSHL (Dr Rob Martienssen - CSHL)
• Launchpad lines (Dr Paul Muskett - John Innes
  Centre)

• T-DNA Insert populations added recently
• Salk T-DNA lines (Dr. Joseph Ecker Salk
  Institute) 60,000.

Identifying the location of insertions   By
homology searching these insert sequences against
Arabidopsis sequences in EMBL it is possible to
identify their putative location. Given a
complete Arabidopsis genome it should be possible
to identify and verify the position of all insert
sequences. Results of homology searches can be
searched by keyword from the NASC catalogue
(http//arabidopsis.info). Graphical displays of
sequences containing putative insertions can be
viewed in AGR (http//ukcrop.net/agr).
APETALA3 gene showing the putative location of
SINS insertion 01_41_07b
Identifying an insertion in your sequence NASC
provides a homology searching facility
(http//arabidopsis.info/blast.html) that allows
users to search sequences against Arabidopsis
insert sequences. The results page links directly
into the catalogue to facilitate ordering
insert-containing lines, and also into AGR which
shows all homologies for a particular insert
sequence.
Results of a BLAST search against Arabidopsis
insert sequences
InsertWatch http//arabidopsis.info/insertwatch
Automated searching of new sequenced insert
populations InsertWatch allows users to submit
sequences to be searched against new sequenced
insert populations as soon as they are released.
If a match is found the results are emailed to
the user, which include links into the catalogue
and into AGR.
http//arabidopsis.info/insertwatch
NASC