2015-08-21 - No of GABI-Kat stocks distributed by stock centres

 

The figure below illustrates the number of order processes concerning GABI-Kat stocks at the European stock center NASC and at ABRC in the USA that took place over time.

 

GK-lines-distributed-NASC-ABRC-2015




2005-06-24 - GABI-Kat T-DNA insertion lines will become freely available

 

In short:
- Seeds for confirmed GABI-Kat lines are to be transferred to NASC.
- Lines still to be confirmed are available from GABI-Kat for a fee of 100,- EUR per line after signing a disclaimer.
 

In the context of the German Plant Genome Research Program GABI (Genomanalyse im biologischen System Pflanze), the GABI-Kat project has produced T-DNA insertion mutants for Arabidopsis thaliana which were subsequently characterized by generating flanking sequence tags (FSTs).

GABI-Kat was initiated at the Max-Planck-Institute of Plant Breeding Research and aims to generate 90,000 T-DNA transformed lines for the sequenced accession Columbia (Col-0). Seeds of single lines (T2 seeds from T1 plants) were harvested, and genomic DNA from T1 plants and was extracted to produce FSTs from their insertion sites by a linker-ligation-PCR based approach. The FST data are then mapped to the genome and the results are made available both via the internet (http://www.gabi-kat.de/), and as a bulk download file for integration into for example SIGnAL or FLAGdb++. Insertion lines can be ordered via a web form, and seeds (usually T2) of confirmed insertion lines are delivered to users.

The GABI program was a private-public partnership that was funded by the BMBF (German Federal Ministry for Education and Research) and the WPG (Business Platform promoting GABI Plant Genome Research e.V.).

The funding partners and the MPG are now happy to announce that GABI-Kat lines will become freely available to the international research community. GABI-Kat lines that have been confirmed will be transferred to NASC as sets of T3 seed harvested from a segregating family of single T2 plants. This will allow direct user access to potentially homozygous material for a given insertion line.

In addition to accessing characterised lines via the stock center, users can order insertion lines that are not (yet) available from NASC directly from GABI-Kat. If confirmed, these lines will be delivered for a fee of 100,- EUR per line after signing a disclaimer.

The transfer of lines from GABI-Kat to NASC has already been initiated and will continue until the end of the GABI-Kat project.

A German press release on this topic was available at the MPG website (meanwhile removed). 

 

Websites:

GABI-Kat: http://www.gabi-kat.de/
GABI program: http://www.gabi.de/
MPI of Plant Breeding Research: http://www.mpiz-koeln.mpg.de/

What does the name GABI-Kat stand for?

 

Koelner Dom Arabidopsis thaliana T-DNA
Kölner Dom Arabidopsis thaliana (picture from Ulrich Melchers Web-Textbook "Molecular Genetics")

 

Kölner

 

Arabidopsis

 

T-DNA lines

The name "GABI-Kat" was chosen because we are funded by GABI (German plant genomics research program), because of the acronym "KAT" as explained above, and because we want to katalyze gene function search.
Although the project is carried out since January 2007 at Bielefeld University (see GABI-Kat history), the acronym was kept. Infomation about the city of Bielefeld can be found here.

SimpleSearch database version information

 

15.08.2016  
GK release 28 (from 77,034 lines with genome hits: 23,582 gene hits, 14,235 CDSi hits). 
- Hit detection based on TAIR9 (still up-to-date) pseudochromosome sequences and Araport11 annotation.
- See FAQ 9 for our current definition of "gene hits". 
- 62.23 % of all A. thaliana nuclear genes are hit (gene hits, protein coding and RNA-encoding genes counted); 
- 75.42 % of A. thaliana nuclear protein coding genes are hit (gene hits, protein coding genes counted); 
- 51.87 % of A. thaliana nuclear protein coding genes are hit (CDSi hits counted); 
- 13967 lines had been sent to NASC on 2016-08-15. The current number of donated lines is presented here.
Note5: The Araport11 annotation contains 37,898 nuclear genes in total, including 27,445 nuclear protein coding genes.
Note6: Pseudogenes were now excluded as targets when evaluating gene hits and CDSi hits. The current release contains 1,062 lines with hits in the 941 pseudogenes reported by Araport11. 
13.05.2014  
GK release 27 (from 72,302 lines with genome hits: 22,515 gene hits, 14,253 CDSi hits). 
- Hit detection based on TAIR9 (= TAIR10) pseudochromosome sequences and TAIR10 annotation.
- See FAQ 9 for our current definition of "gene hits". 
- Pseudogenes included as target when evaluating gene hits and CDSi hits;
- 67.57 % of all A. thaliana genes are hit (gene hits, TS2TE hits and promoter hits counted); 
- 74.49 % of A. thaliana protein coding genes are hit (gene hits. TS2TE hits and promoter hits counted); 
- 52.39 % of A. thaliana protein coding genes are hit (CDSi hits counted); 
- 12,874 lines had been sent to NASC on 2014-05-13. 
10.04.2014  
GK release 26 (from 72,302 lines with genome hits: 21,453 gene hits, 13,435 CDSi hits). 
- Hit detection based on TAIR9 (= TAIR10) pseudochromosome sequences and TAIR10 annotation.
- See FAQ 9 for our current definition of "gene hits". 
- Pseudogenes included as target when evaluating gene hits and CDSi hits;
- 64.38 % of all A. thaliana genes are hit (gene hits, TS2TE hits and promoter hits counted); 
- 71.65 % of A. thaliana protein coding genes are hit (gene hits. TS2TE hits and promoter hits counted); 
- 49.39 % of A. thaliana protein coding genes are hit (CDSi hits counted); 
- 12,674 lines had been sent to NASC on 2014-04-10.
01.03.2012  
GK release 25 (from 72,064 lines with genome hits: 21,381 gene hits, 13,337 CDSi hits). 
- Hit detection based on TAIR9 (= TAIR10) pseudochromosome sequences and TAIR10 annotation.
- See FAQ 9 for our current definition of "gene hits". 
- Pseudogenes included as target when evaluating gene hits and CDSi hits;
- 64.2 % of all A. thaliana genes are hit (gene hits, TS2TE hits and promoter hits counted); 
- 71.4 % of A. thaliana protein coding genes are hit (gene hits. TS2TE hits and promoter hits counted); 
- 49.0 % of A. thaliana protein coding genes are hit (CDSi hits counted); 
- 10,239 lines had been sent to NASC on 2012-03-01.
07.03.2011  
GK release 24 (from 71,239 lines with genome hits: 18,908 gene hits, 13,038 CDSi hits).
- Hit detection based on TAIR9 pseudochromosome sequences and TAIR10 annotation.
- New definition of "gene hits": insertion between transcription start and polyA addition site (TS2pA - but see Note4 below/TS2TE). Only if this information is not available in the annotation data, 300 bp upstream of ATG to 300 bp downstream of STOP are considered. This change reduces the number of "gene hits". CDSi hit: insertion between ATG to STOP (CDS plus introns).
- Pseudogenes included as target when evaluating gene hits and CDSi hits;
- 56.3 % of all A. thaliana genes are hit (gene hits including TS2TE hits counted);
- 62.0 % of A. thaliana protein coding genes are hit (gene hits including TS2TE hits counted);
- 47.6 % of A. thaliana protein coding genes are hit (CDSi hits counted);
- 8,646 lines had been sent to NASC on 2011-03-07. 
Note2: The TAIR10 annotation dataset contains 33,602 genes in total, including 27.416 protein coding genes.
Note3: The GK release determines which lines and FSTs are available in SimpleSearch. If we produce new FSTs for our lines or even new lines, a new release is required to get these items into SimpleSearch. However, the data values for the items in the database are updated automatically once every 24 hrs from our internal LIMS (lab information managment system). This affects for example new segregation data, new NASC donations and NASC ID's, new confirmation sequences and so on. 
Note4: After the release 24 was made available, we changed the term TS2pA (from transcription start to polyA addition site) to TS2TE (from transcription start to transcript end) to also cover not polyadenylated ncRNA transcripts. 
04.08.2008  
GK release 23v2 (from 64244 lines with genome hits: 17,016 gene hits, 12,298 CDSi hits). 
- 6,018 lines have been sent to NASC.
30.11.2007  
GK release 23 (from 64,244 lines with genome hits: 17,016 gene hits, 12,298 CDSi hits).
- 5,551 lines have been sent to NASC .
20.03.2007  
GK release 22 (from 64,339 lines with genome hits: 17,018 gene hits, 12,301 CDSi hits).
- 4,293 lines have been sent to NASC.
25.06.2006
  
GK release 21 (from 63,812 lines with genome hits: 16,939 gene hits, 12,239 CDSi hits).
- 3,509 lines have been sent to NASC.
- New search interface allows searching for line ID or FST GenBank accession number.
- Genetic segregation and confirmation sequencing data included.
20.04.2006
  
GK release 20 (from 63,812 lines with genome hits: 16939 gene hits, 12,239 CDSi hits).
- 2,282 lines have been sent to NASC.
15.12.2005
  
GK release 19 (from 6,2697 lines with genome hits: 16,804 gene hits, 12,129 CDSi hits).
- 1,751 lines have been sent to NASC.
15.09.2005
  
GK release 18 (from 62,524 lines with genome hits: 16,782 gene hits, 12,112 CDSi hits).
- Information concerning lines transferred to NASC included (example: At2g31180).
- 712 lines have been sent to NASC.
01.02.2005
  
GK release 17 (from 61,768 lines with genome hits: 16,664 gene hits, 11,987 CDSi hits).
15.09.2004
  
GK release 16 (from 60,741 lines with genome hits: 16,558 gene hits, 11,883 CDSi hits).
- Hit detection based on TIGR sequence and BAC annotation v5.
01.05.2004
  
GK release 15 ** (from 60,527 lines with genome hits: 17063 gene hits, 12,304 CDSi hits).
15.03.2004
  
GK release 14 ** (from 55,138 lines with genome hits: 16214 gene hits, 11,560 CDSi hits).
01.02.2004
  
GK release 13 ** (from 52,250 lines with genome hits: 15,742 gene hits, 11,127 CDSi hits).
15.12.2003
  
GK release 12 ** (from 47,701 lines with genome hits: 14,914 gene hits, 10,425 CDSi hits).
05.10.2003
  
GK release 11 (from 44,358 lines with genome hits: 14,047 gene hits, 9,726 CDSi hits).
- Hit detection based on MAtDB release version 11092003.
01.08.2003
  
GK release 10 (from 36,486 lines with genome hits: 12470 gene hits, 8,493 CDSi hits).
01.07.2003
  
GK release 9 (from 36,206 lines with genome hits: 12382 gene hits, 8,425 CDSi hits).
01.06.2003
  
GK release 8 (from 35,302 lines with genome hits: 12191 gene hits, 8,270 CDSi hits).
01.03.2003
  
GK release 7 (from 31,734 lines with genome hits: 11350 gene hits, 7,599 CDSi hits).
15.02.2003
  
GK release 6 (from 26,375 lines with genome hits: 9,862 gene hits, 6,458 CDSi hits).
- New definition of "gene hits": insertion between 300 bp upstream of ATG to 300 bp downstream of stop. CDSi hit: insertion between ATG to stop (CDS plus introns).
- Hit detection based on MAtDB release version 11012003.
01.12.2002
  
GK release 5 (from 26,350 lines with genome hits: 8,230 gene hits, old definition).
01.10.2002
  
GK release 4 (from 24,138 lines with genome hits: 7,635 gene hits, old definition).
- Hit detection based on MAtDB release version 17092002.
01.09.2002
  
GK release 3 (from 22,825 lines with genome hits: 7,200 gene hits, old definition).
- A new page show the genes and FSTs graphically, search result page rearranged.
01.08.2002
  
GK release 2 (from 17,767 lines with genome hits: 5,835 gene hits, old definition).
- Hit detection based on MAtDB release version 26072002.
01.06.2002
  
Opening of the GABI-Kat homepage.
- GK release 1 (from 13,531 lines with genome hits: 4,642 gene hits, old definition).
- Hit detection based on MAtDB release version 11052002.

 

** Note1: There were 664 genes which were only annotated in TIGR and did not overlap with MAtDB gene annotations; these were incorporated in the dataset for hit detection.

Development, timeline and output of GABI-Kat 

 

Since January 2015, some people from the "Plant Genome Research" group at Bielefeld University (Weisshaar lab) try to keep the GABI-Kat community service alive. However, due to lack of hands and time, we are slower than before.

The figures below illustrate the output that was generated by GABI-Kat until 2014. Scroll down to read about GABI-Kat history.



Figure 1: Progress of donation of confirmed CDSi alleles to NASC
 

GK-CDSi-alleles-to-NASC

The green dotted line represents the number of genes for which CDSi hit predictions are available in the GABI-Kat collection. Donation to NASC started in 2005. The gray dashed line illustrates the number of lines, which would have been available at NASC if the donation would have started directly at the begin of the GABI-Kat project.

 



Figure 2: No of finally resolved insertion predictions

GK-finally-resolved-insertion-predictions-2015

 

In this graph the number of insertion site predictions is shown for which a final result of the confirmation process was generated. This means that the confirmation attempt was either successful or failed and the insertion is not addressed anymore. 



GABI-Kat was initiated at the Max-Planck-Institute of Plant Breeding Research (Cologne, Germany) in the year 1999 and the work started in June 2000. The initial PI's were Bernd Weisshaar, Koen Dekker, Bernd Reiss and Heinz Saedler. Funding was provided by BMBF/PTJ through the GABI programme. By building on experience from the ZIGIA project (which centred on transposons for insertional mutagenesis in A. thaliana, see Dekker et al., 2003; BIOTECHNOLOGIA 4:9-31 - note that the Journal is not published anymore, the link leads to PUB), selection, growth and leaf harvest for DNA extraction from about 90,000 single T-DNA-transformed lines was completed around February 2006. Within GABI-2, the project was continued to moderately increase the number of lines to be analysed (within GABI-1 it was 70,000), to further improve the quality of the mutant population, and to continue to serve the Arabidopsis community with providing confirmed insertion lines.

At the end of December 2006, the project was moved from MPIZ Cologne to Bielefeld University (Chair of Genome Research, Bernd Weisshaar) where GABI-Kat-II (or GKat) started on the 1st of January 2007. At the same time, the project was extended until December 2008. The main focus of this extension was to transfer more lines to NASC, and to confirm all lines that contain insertions in genes that are not hit in other populations.

At the end of 2008, there was first a continuation of the running grant until June 2009, and then an extension of the project until June 2011. The goal was to confirm additional lines and transfer them to NASC. In parallel, the community service continued and the FST collection was re-annotated with new data from TAIR.

In 2011, there was first a continuation of the running grant until December 2011, and then an extension of the project until June 2014. New FSTs that had been generated from low-coverage parts of the collection and re-annotation according to TAIR10 of all existing FSTs allowed to extend the number of predicted insertions. The community service and donation to NASC continued.

In March 2014, the GABI-Kat grant was extended to the end of December 2014. Although we got very nice support from quite some users, and also strong support from ABRC and NASC, the grant was not renewed or extended. Anyway, we thank BMBF/PtJ for many years (many more than usual for a "normal" project) of very helpful support!