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Annotating Arabidopsis

Now that the Arabidopsis thalianagenome 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 RIKENArabidopsisFull-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 Arabidopsisgenes is 17,956.


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

  2. Sciencexpress, []

  3. RIKEN Institute , []

  4. Plant functional genomics research group, []

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

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Weitzman, J.B. Annotating Arabidopsis. Genome Biol 3, spotlight-20020326-02 (2002).

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