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First survey of the wheat chromosome 5A composition through a next generation sequencing approach

TitleFirst survey of the wheat chromosome 5A composition through a next generation sequencing approach
Publication TypeArticolo su Rivista peer-reviewed
Year of Publication2011
AuthorsVitulo, N., Albiero A., Forcato C., Campagna D., Dal Pero F., Bagnaresi P., Colaiacovo M., Faccioli P., Lamontanara A., Šimková H., Kubaláková M., Perrotta Gaetano, Facella P., Lopez L., Pietrella M., Gianese G., Dolezel J., Giuliano Giovanni, Cattivelli L., Valle G., and Stanca A.M.
JournalPLoS ONE
Keywordsarticle, Biology, Brachypodium, chromosome 1, chromosome 12, chromosome 2, chromosome 3, chromosome 4, chromosome 5A, chromosome 8, chromosome 9, chromosome structure, Chromosomes, Computational Biology, Conserved Sequence, contig mapping, controlled study, DNA Transposable Elements, expressed sequence tag, Flow cytometry, fluorescence in situ hybridization, gene amplification, gene control, gene order, gene sequence, Genes, genetics, high throughput sequencing, High-Throughput Nucleotide Sequencing, Karyotype, matrix attachment region, methodology, microRNA, MicroRNAs, nonhuman, nucleic acid amplification, Nucleic Acid Amplification Techniques, nucleotide sequence, Plant, plant chromosome, plant gene, plant genetics, protein assembly, pyrosequencing, rice, Sequence Analysis, sorghum, synteny, transposon, Triticum, Triticum aestivum, wheat

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. © 2011 Vitulo et al.


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Citation KeyVitulo2011