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Annotating Arabidopsis

Jonathan B Weitzman

Genome Biology 2002, 3:spotlight-20020326-02  doi:10.1186/gb-spotlight-20020326-02

The electronic version of this article is the complete one and can be found online at:


Published:26 March 2002

© 2002 BioMed Central Ltd

Research news

Now that the Arabidopsis thaliana genome has been sequenced, plant biologists are turning their efforts to genome annotation. In a report published on the Sciencexpress website, Motoaki Seki and colleagues from the RIKEN Institute in Japan, describe a large-scale analysis of full-length Arabidopsis cDNA libraries (Sciencexpress, 21 March 2002 10.1126/science.1071006). They isolated over 150,000 RIKEN Arabidopsis Full-Length (RAFL) cDNA clones, sequenced the ends and clustered them into almost 15,000 non-redundant groups. To generate the clones they constructed 19 cDNA libraries from plants grown under various conditions of stress, hormone and light. To optimize library construction they used the biotinylated CAP trapper method, using trehalose-thermoactivated reverse transcriptase combined with a single-strand linker ligation step, and normalization and subtraction procedures. They also created a database of promoter sequences upstream of RAFL clones. Amongst the clones were 837 that had been missed by previous annotation efforts; this project therefore makes a significant contribution to attempts to annotate the Arabidopsis genome. The current tally of experimentally confirmed Arabidopsis genes is 17,956.

References

  1. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

    PubMed Abstract | Publisher Full Text OpenURL

  2. [http://www.sciencexpress.org] webcite

    Sciencexpress

  3. [http://www.riken.go.jp] webcite

    RIKEN Institute

  4. [http://www.gsc.riken.go.jp/Plant/index.html] webcite

    Plant functional genomics research group

  5. High-efficiency full-length cDNA cloning by biotinylated CAP trapper.

    PubMed Abstract | Publisher Full Text OpenURL