Abstract
Wheat is one of the world's most important crops and is characterized by a large polyploid genome. One way to reduce genome complexity is to isolate single chromosomes using flow cytometry. Low coverage DNA sequencing can provide a snapshot of individual chromosomes, allowing a fast characterization of their main features and comparison with other genomes. We used massively parallel 454 pyrosequencing to obtain a 2x coverage of wheat chromosome 5A. The resulting sequence assembly was used to identify TEs, genes and miRNAs, as well as to infer a virtual gene order based on the synteny with other grass genomes. Repetitive elements account for more than 75% of the genome. Gene content was estimated considering non-redundant reads showing at least one match to ESTs or proteins. The results indicate that the coding fraction represents 1.08% and 1.3% of the short and long arm respectively, projecting the number of genes of the whole chromosome to approximately 5,000. 195 candidate miRNA precursors belonging to 16 miRNA families were identified. The 5A genes were used to search for syntenic relationships between grass genomes. The short arm is closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; the long arm to regions of Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosomes 9 and 3. From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome.
Highlights
Wheat is one of the world’s most important crops, but despite its economic importance progress in wheat genomics has been slow due to its large and complex genome
The arms were sorted as telocentric chromosomes 5AS and 5AL from a double ditelosomic line
The use of telosomic stocks enables the dissection of the huge wheat genome into small parts which facilitates its analysis and mapping [3]
Summary
Wheat is one of the world’s most important crops, but despite its economic importance progress in wheat genomics has been slow due to its large and complex genome. Several studies, coordinated by the International Wheat Genome Sequencing Consortium (http:// www.wheatgenome.org) are in progress with the aim of obtaining and characterizing the wheat genome. When flow-sorted chromosomes are subjected to low-coverage massively parallel DNA sequencing, a snapshot of single chromosomes can be produced even in species with a large genome. In the first study of this type, Mayer et al [6] characterized repetitive elements and genes in the barley chromosome 1H, identified syntenic regions with genomes already sequenced and produced a linearly ordered high-resolution gene inventory of the chromosome
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