| Bread wheat (T.aestivum) is one of the most important crops in the world, yet studies about it lags far behind small genome organisms, such as O. sativa. A. thaliana, etc. Up to date, only a few wheat genes were cloned because of its large genome (1.6 1010bp) and redundant repeat sequences (about 90 % ) . As most of clones from full-length cDNA library contained not only the CDS but also the UTRs of 5' and 3' regions, which facilitate the progress of later researches such as sequencing, structural and functional analysis, the full-length cDNA library is regarded as an effective approach to discover new genes in large scale.Based on the published Cap-trapper method, we improved some of its steps and built our own full-length cDNA construction platform. Using the improved Cap-trapper method, we have constructed three full-length cDNA libraries of wheat's A, B, D genome donors T.urartu, Ae.speltoides ssp speltoide and Ae.tauchii ssp strangulata. Results indicated that the number of clones and recombination rates of these libraries all met standards of library construction. The rates of full-length cDNA clones in the three libraries were 70%, 89.6% and 70%, respectively.Gene functional annotation showed that 1584 genes were full-length and 1346 genes were new full-length genes in the 2089 genes. Among the full-length new genes, 569 were from A genome, 553 from S genome and 468 from D genome.Codon usage bias is one of the characters of organism which was formed in the evolution process. Researches indicated that a lot of factors affected codon usage, such as the content of G+C, the length of genes, the abundance of tRNA, etc. We analyzed the codon usage of 2089 genes in wheat's three genome donors. The statistical results suggested that there were no difference of the codon usage among the three genomes, yet the usage bias was obvious in single genome, for example, the frequencies of AAG (Lys), GAG (Glu), GCC (Ala) were more than 35%o, the frequency of GCC (Ala) was even more than 45%o; in addition, there were 3 codons whose frequencies were more than 30%o and 12 codons were more than 20%o . Comparing with the codon usage in rice, we found the diversity between the two crops. In the amino acids with 4-6 synonymous codons, the third nucleotides of the optimal codon in rice were apt to U and C, yet in wheat they were apt to G and C.Comparative genomics is one important part of genomics, people can learn much by comparing the different organism at different hirrarchy, and make it possible to discover the energy of evolution. We got 22 groups of orthologous genes after multi-screening the sequencing results of the three genomes. Based on the phylogeny analysis we found most of genes from A, D genomes clustered in same branches, which meaned that the relationship of A and D genomes were much closer among A, S, D genomes. EST analysis and SNPs mining results also got the same conclusion.Single nucleotide polymorphisms (SNPss) is another research focus with the characters of large amount, high stability, wide distribution, easy, high-throughput detection and wide application. Using the 2089 genes as origin templates, we "fished out" 1296 SNPs with autoSNPsFinder from the wheat dbEST in Genbank. 397 SNPs were from A genome, 322 SNPs from S genome and 420 SNPs from Dgenome. The number of common SNPs of A and D genomes was 154. The SNPs shared by A and S, S and D, A, S and D were only 1 respectively. The average substitution rate in wheat was 0.914%o, which was much similar to that of soybean (0.97%o) , yet different with the maizes (6.3%o).
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