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Common wheat Triticum aestivum is a hexaploid plant of the Poaceae family. It came from the convergence of three diploid ancestors. The total number of base pair is 15,966 Mbp/haploid cell and the sub-genome size is 5600 Mbp. Hexaploid bread wheat, Triticum aestivum L. has an estimated genome size 1.6 - 1010 bp. Total bacterial artificial chromosome (BAC) number in TIGR annotation is 67 and there are 582 total gene models. 2220 bp constitutes one average gene size while the average exon number is 2.8 with average length of 318. Average GC content of an exon is 55.9%. Similarly, the average intron number is 1.8 with average size of 694 bp that holds 43.9% of total GC content.
Proportion of G-C content: Average GC content of an exon is 55.9%. Similarly, the average intron number is 1.8 with average size of 694 bp that holds 43.9% of total GC content in wheat.
Duplicated genes: Duplicated genes may result from either polyploidization (homoeologous genes) or segmental chromosome duplications (paralogous genes). Pseudogenes are the nonfunctional or low functional copies of genes duplicated elsewhere in the genome. The duplicated genes couldn't have same functions as the original genes. Duplications of DNA fragments in the genome are often the result of Double -strand break (DSB) repair whereby a copy of the foreign DNA is used as filler to repair the break. Since the rate of gene duplication is variable, it's hard to predict the number of duplicated genes in wheat.
Repetitive sequences: The Repetitive DNA fraction is estimated to be about 80% of the genome and the non-repetitive DNA fraction is estimated to be about 17% of the wheat genome.
The genomes of all eukaryotes contain a class of sequences, known as microsatellites. The analysis of microsatellites is based on the polymerase chain reaction (PCR), which is much easier to perform than RFLP analysis. It shows a much higher level of polymorphism and informativeness in hexaploid wheat than any other marker system.
Transposon sequences: The repetitive, non-genic regions of wheat, as in many plant genomes, primarily consist of transposable elements (TEs) and to a much lesser extent of pseudogenes.In wheat, rapid rates of transposon insertion and deletion yields a rapid turnover of intergenic regions that affects neighbouring genes. In wheat, about 80% of the genome consists of repeated sequences and 68% of transposable elements.
Junk DNA: Though the wheat genome is large, most of the DNA is not useful. The study shows that about 97% of the wheat genome is junk DNA, or repeated sequences. Only 3% of genome actually code for traits expressed in the wheat plant.
Describe advantages and disadvantages of the model genomes that are used for the species that you are working on.
Due to the absence of complete genome sequence, gene content and gene order, wheat is compared with the completely sequenced model grass genomes of rice. Rice (Oryza sativa) is a model plant species for many cereal species including wheat. It is a diploid species of Ehrhartoideae family and its genome belongs to AA group. The genome size of rice is very small (450 Mbp) and it is less complex than wheat. There are 12 chromosomes pairs in the rice genome and it contains only about 50 % of the repeated sequence. It is the first crop plant whose complete genetic sequence/ genome has been compiled and placed in computer data banks around the world. Rice is selected as a model plant species for cereals genomics because of the following reasons:
It has relatively well conserved colinearity with other cereals.
Comparatively small size of its genome relative to other cereals.
The availability of tools for functional genetics: Transposon- and T-DNA-tagged rice populations exist, and the microarray technology for studying mRNA expression profiles is available.
The advantages and the disadvantages of the rice genomes for wheat species are listed below:
The availability of rice genome sequence data has allowed for an in-depth comparison of genes.
Transposable elements (TEs) are nearly equal among the different cereal genomics including wheat.
The same genes exist in the same order on a chromosome in rice and wheat.
Many rice genes share nucleotide identity of 80% or more with wheat.
Rice genes are homologous among various cereal gene families. Thus the studies on the functions of genes or proteins from one cereal could lead to elucidation of the functions of orthologous genes/proteins in other cereals.
Conservation of gene identity and colinearity between wheat and rice depends on the rate of genome/gene evolution and rearrangement in both species.
Many genes present in the rice are not present at the orthologous position in wheat.
Many studies show that Brachypodium, belonging to subfamily Pooideae (like wheat), is better model than rice. Because the colinearity between Barchypodium and wheat is better than wheat and rice.
Changes in sequence such as insertion, deletion, duplication, and translocation can further complex the use of rice genome for cross-species comparison.
Many gene models in rice are not yet completely reliable making it risky to compare them with other genes in the database to analyze the function of the genes.
Though rice has a fully sequenced genome, it is still difficult to calculate the gene number because many genes are likely to be remnants of transposable elements.