Vitulo, N., Albiero, A., Forcato, C., Campagna, D., Dal Pero, F., Bagnaresi, P., Colaiacovo, M., Faccioli, P., Lamontanara, A, Šimková, H., Kubaláková, M., Perrotta, G., Facella, P., Lopez, L., Pietrella, M., Gianese, G., Doležel, J., Giuliano, G., Cattivelli, L., Valle, G., Stanca, A.M.
PLoS ONE
6 (10):
e26421,
2011
Klíčová slova:
Abstrakt:
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.
Fulltext: kontaktujte autory z ÚEB
Autoři z ÚEB: Jaroslav Doležel,
Marie Kubaláková,
Hana Šimková
Čeština
English