Collection of Flanking sequence Tags (FSTs)

The Brachypodium genomic sequences flanking the T-DNA inserts are known as Flanking Sequence Tags (FSTs). FSTs inform on the position of the T-DNA inserts into the plant genome. When a T-DNA insertion occurs into a Brachypodim gene, the FST characterises the distrupted gene. This gene may have a known or putative function.


FST Display in Genome Browsers:  

link to modelcrop genome browser
 The position of the FSTs charaterising the T-DNA inserts in the Brachypodium genome sequence is displayed in the Modelcrop genome browser.

Example of FST display in Modelcrop genome browser (this FST characterises a T-DNA insertion in an aquaporin gene in line BdAA235). Note: when using Modelcrop for the first time, agree with 'Terms & Conditions' then select the following tracks 'Gene predictions - All on' and 'Other features - FST JIC '.

Quick information guide regarding the display of BrachyTAG FSTs in genome browsers such as Modelcrop.org:

  • All BrachyTAG FSTs start with the 3 letters “JIC” (i.e. John Innes Centre).
  • BrachyTAG FST names provide both FST and T-DNA plant line information. For example “JIC00100_115” indicates that the FST sequence “00100” has been retrieved from the T-DNA plant line “115”.
  • BrachyTAG FSTs are free of duplicated or consecutive sequence reads .
  • More than one FST can be retrieved from a single T-DNA plant line.
  • BrachyTAG analyses the regions flanking both sides of the T-DNA insertion(s). Therefrore, for many T-DNA insertions (approx. 1/3) FSTs are available from both sides of the T-DNA. This validates the genomic location and informs on how much Brachypodium genomic DNA has been deleted during the T-DNA insertion.  

Quick SEARCH guide when using Modelcrop.org:

  • To SEARCH for all the FSTs recovered from a given T-DNA line: type “JIC*_115” in the genome browser search field to recover all FSTs from line "115".
  • To SEARCH for all FSTs recovered in a given Brachypodium gene: type “Bradi1g34170” in genome browser search field to recover all FSTs in Bradi1g34170.
  • To SEARCH for all FSTs recovered from a given region: type “Bd3:53210000..53700000” in genome browser search field to recover all FSTs from 53210000 to 53700000 on Bd3. [Tip: when searching FSTs over large genomic regions, only turn on “predicted transcripts” and “FST JIC” tracks].
  • To SEARCH for information on tagged gene: click on predicted transcript in the Modelcrop main browser image display to access “Location”, “Gene” and “Transcript” information in EnsemblPlants
  • To SEARCH for putative function of tagged gene in 3 clicks: 1. Predicted transcript (in Modelcrop main browser image display) / 2.  "Gene" tab (among the top tabs “Location”, “Gene” and “Transcript” in EnsemblPlants) / 3. Orthologues (left window in “Gene” tab in EnsemblPlants).


FST Display in Public Databases:
 FSTs are available from public databases. These databases are accessible online using freely available web sites such as the European Bioinformatic Institute (EMBL-EBI) or the National Centre for Biotechnology Information (NCBI)

Example of FST display in GenBank (this FST characterises a T-DNA insertion in an aquaporin gene in line BdAA235).

BrachyTAG, Brachypodium flanking sequence tag ( FST)

 

Table: Summary of Brachypodium Flanking Sequence Tags (FSTs) produced by the BrachyTAG project.

Number
of FSTs
GenBank acc_Nb
(date batch submission)
FSTs in genome browser
(date batch submission)
Number of tagged genes*
Project reference – Sponsor
1,005 - ongoing EF165098 (Jan 2007 )
ER987315 to ER987358 (Aug 2007)
ER987418 to ER987435 (Aug 2007)		 37 (Feb 2010)
861 (Apr 2010)

365
 C0612 - BBSRC (UK)
CT039 - Marie Curie (EU)

* Known genes and putative orthologues of tagged genes . Table updated April 2010