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Comprehensive collection of transcripts as reference of gene annotation in common wheat

Research Objective

We aim to collect comprehensively full length cDNAs in common wheat for annotation of functional genes, and assign those transcripts into each homoeologous chromosome of A, B and D genomes.

What we are doing

Fig.2 Distribution of the gene clusters showing homology with those of other graminous plants We systematically prepared a comprehensive collection of ESTs from the various tissues that develop during the wheat life cycle and from tissues treated with environmental stresses. We also carried out a systematic survey of full length cDNA library constructed with the CAP-trapper method. By screening independent cDNA clones with the bio-informatics, the nucleotide sequences of those selected full-length cDNAs have been completely determined with the next-generation sequencer (Roche 454 GS-FLX Titanium) in addition to the ordinary Sanger-method. Until now, the 21,408 sequence data of the full-length cDNAs are available.
805,544 EST data of common wheat including the full-length cDNA sequences were bio-informatically clustered into the 41,003 gene clusters, in which the 27,943 genes had the counterparts in the grass genomes, but the remaining 13,060 were estimated to be wheat-specific. Each gene cluster contains a number of homoeologues. These homoeologues are assigned into each of three genomes, i.e., A, B and D using the contigs assembled with the comprehensive sequence data obtained by the RNA seq (Illumina Hiseq 2000) from each diploid ancestor of common wheat (Triticum urartu, Aegilops speltoides, and Ae. tauschii). Genome and/or chromosome locations of these homoeologues are also deduced using the genome sequence data of Chinese Spring wheat obtained by the shot-gun sequencing or survey sequencing of each chromosome in Chinese Spring wheat.

Fig.1 Pipeline for gene clustering from comprehensive ESTs including the full-length cDNAs


  • Yasunari OGIHARA, Project Leader
  • Kanako KAWAURA
  • Kohei MISHINA


  • Jun KAWAI
  • Hiroshi TARUI

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