Use of Mutants from T‐DNA Insertion Populations Generated by High‐Throughput Screening

Stracke, Ralf; Huep, Gunnar; Weißhaar, Bernd

doi:10.1002/9783527629398.ch3

Cited by 2 publications

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“…The size of the amplicons was checked by agarose gel electrophoresis. Samples were purified for sequencing by ExoSAP-IT (78201.1.ML ThermoFisher Scientific) treatment as described [ 40 ]. Sanger sequencing on ABI3730XL was applied to reveal the entire sequences as described [ 41 ].…”

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confidence: 99%

Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence

2017

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ObjectiveThe Arabidopsis thaliana Niederzenz-1 genome sequence was recently published with an ab initio gene prediction. In depth analysis of the predicted gene set revealed some errors involving genes with non-canonical splice sites in their introns. Since non-canonical splice sites are difficult to predict ab initio, we checked for options to improve the annotation by transferring annotation information from the recently released Columbia-0 reference genome sequence annotation Araport11.ResultsIncorporation of hints generated from Araport11 enabled the precise prediction of non-canonical splice sites. Manual inspection of RNA-Seq read mapping and RT-PCR were applied to validate the structural annotations of non-canonical splice sites. Predictions of untranslated regions were also updated by harnessing the potential of Araport11’s information, which was generated by using high coverage RNA-Seq data. The improved gene set of the Nd-1 genome assembly (GeneSet_Nd-1_v1.1) was evaluated via comparison to the initial gene prediction (GeneSet_Nd-1_v1.0) as well as against Araport11 for the Col-0 reference genome sequence. GeneSet_Nd-1_v1.1 contains previously missed non-canonical splice sites in 1256 genes. Reciprocal best hits for 24,527 (89.4%) of all nuclear Col-0 genes against the GeneSet_Nd-1_v1.1 indicate a high gene prediction quality.Electronic supplementary materialThe online version of this article (10.1186/s13104-017-2985-y) contains supplementary material, which is available to authorized users.

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Section: Main Textmentioning

confidence: 99%

Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence

2017

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“…There are several databases, websites and portals available to start searching for insertion mutants, each with specific advantages and disadvantages ( Kuromori et al 2009 , Stracke et al 2010 , Bolle et al 2011 ). Generally, the basis for these search options are flanking sequence tags (FSTs).…”

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confidence: 99%

Enhancing the GABI-KatArabidopsis thalianaT-DNA Insertion Mutant Database by Incorporating Araport11 Annotation

2016

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SimpleSearch provides access to a database containing information about T-DNA insertion lines of the GABI-Kat collection of Arabidopsis thaliana mutants. These mutants are an important tool for reverse genetics, and GABI-Kat is the second largest collection of such T-DNA insertion mutants. Insertion sites were deduced from flanking sequence tags (FSTs), and the database contains information about mutant plant lines as well as insertion alleles. Here, we describe improvements within the interface (available at http://www.gabi-kat.de/db/genehits.php) and with regard to the database content that have been realized in the last five years. These improvements include the integration of the Araport11 genome sequence annotation data containing the recently updated A. thaliana structural gene descriptions, an updated visualization component that displays groups of insertions with very similar insertion positions, mapped confirmation sequences, and primers. The visualization component provides a quick way to identify insertions of interest, and access to improved data about the exact structure of confirmed insertion alleles. In addition, the database content has been extended by incorporating additional insertion alleles that were detected during the confirmation process, as well as by adding new FSTs that have been produced during continued efforts to complement gaps in FST availability. Finally, the current database content regarding predicted and confirmed insertion alleles as well as primer sequences has been made available as downloadable flat files.

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Use of Mutants from T‐DNA Insertion Populations Generated by High‐Throughput Screening

Cited by 2 publications

References 45 publications

Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence

Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence

Enhancing the GABI-KatArabidopsis thalianaT-DNA Insertion Mutant Database by Incorporating Araport11 Annotation

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