Analysis of genomes, transcripts and genes affected by splicing in bread wheat

Bread wheat (Triticum aestivum L.) is an allohexaploid plant consisting of three genomes (A, B and D) that originated from three ancestral diploid species via multiple hybridizations. Despite the availability of the wheat genome sequence and the related studies conducted, more information about its genome and transcriptome can still be obtained. The aim of this study was to extract descriptive information about wheat genes and transcripts and investigate the similarities and differences of wheat genomes from different points of view such as number of genes and transcripts, gene density, number of introns, alternative splicing, CDS and UTR length, and GC content. Results showed that the gene density in wheat is about 7.5 and the D genome has a higher density than the other two genomes. In addition, despite the difference in the average of genes and introns lengths, high similarities were found in the average of exon, transcripts, and coding region lengths of A, B, and D genomes. Comparison of transcripts and genes represented approximately 80% of the genes contained introns. This comparison also revealed alternative splicing occurred in approximately 16% of the genes. Our study showed most of the splicing sites occurs in the CDS and a small part of the UTR region. By focusing on CDS regions, more abundance of splicing was observed between codons than within codons. It was also shown most of wheat transcripts contain UTR and almost 10% of UTRs contain uORF. Although the amount of GC content of genes, transcripts, introns and UTRs were between 30-80 percent, the relationship between GC content and the length of mentioned cases showed a different pattern. Finally, it could be concluded, despite differences in the origin of bread wheat genomes, many similarities in terms of chromosome length, gene density, alternative splicing and various parameters such as CDS length, UTR length and GC percentage would be seen.