Identification of Standard Transcripts in Common Wheat
We attempted to identify standard transcripts in common wheat from the EST data; our data for 805,544 ESTs, including those for FLcDNAs, were assembled in each of the ten strains of common wheat. After assembly with MIRS (chevreux. org/projects_mira.html), 191,988 contigs and 326,851 singlets were obtained. The resultant contigs and singlets were clustered by the CD HIT software by setting the criteria at an identity of 99.5 % to obtain homoeologs (6×), and 95 % to obtain homologs (2×). Consequently, 162,874 gene clusters (2×) were grouped. Out of these clusters, 81,694 clusters were matched to expressed genes of barley (Matsumoto et al. 2011), Brachypodium (Mochida et al. 2013), and rice ( ricegaas.dna.affrc.go.jp/rgadb/). By removing redundant results, 27,943 gene clusters that had homologies with Poaceae transcripts could be established at the diploid level; 81,180 clusters had no homologs among cereal genomes. Therefore, we conducted a “blat search” against 5× draft wheat genome sequences (Brenchley et al. 2012); 54,446 clusters were found to have homologies with the wheat genome sequences. By grouping these clusters at 80 % identity, 13,060 wheat-specific genes were obtained. From these analyses, 41,003 gene groups were clustered in wheat. Out of the 41,003 genes, 27,943 wheat genes had common homologies to Poaceaeexpressed genes.
Chromosome Assignment of Expressed Genes in Common Wheat
We assigned these expressed homoeologs to each chromosome based on the “Survey sequence” organized by the International Wheat Genome Sequence Consortium (wheatgenome.org/). From this rough assignment, we can estimate the number of expressed genes from each chromosome and/or chromosome arm (Fig. 10.3). Chromosome 3B and 5BL were highly expressed. Conversely, genes located on 6B, which is the Japanese sequencing target, were less commonly expressed.
Snapshots of gene expression profiles in the wheat life cycle and/or in response to environmental stresses were developed; 22,519 sequence-verified full-length cDNAs were obtained. Of these, 77.4 % were assigned into the A, B, and D genomes with the RNAseq data from their diploid ancestors. We obtained 284,822 homoeoclusters (6×) from 805,544 ESTs of common wheat. These homoeo-clusters were classified into 27,943 (Poaceae common) and 13,060 (wheat specific) gene groups
Fig. 10.3 Chromosome assignments of wheat-expressed genes by using the Chinese Wheat “Survey-sequences” of IWGSC
(2×). In total, 41,003 wheat transcripts (2×) were classified; 284,822 homoeoclusters were assigned into 21 chromosomes using “Survey-sequences” from the IWGSC.
Thus, the words of Prof. Kihara (1946), “The history of the earth is recorded in the layers of its crust. The history of all organisms is inscribed in the chromosomes” hold true even now, in the genomics era.
Acknowledgments We are grateful to all members of KOMUGI, Wheat Genomics Consortium of Japan. Without their contributions, this project could not have been carried out. This work was supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan and the Ministry of Agriculture, Forestry and Fisheries of Japan.