January 15-19, 2011
Town & Country Convention Center
San Diego, CA
Nicola Vitulo1 , Alessandro Albiero1,2 , Claudio Forcato1 , Davide Campagna1 , Francesca Dal Pero2 , Paolo Bagnaresi3 , Moreno Colaiacovo3 , Primetta Faccioli3 , Antonella Lamontanara3 , Hana Simkova4 , Marie Kubaláková4 , Gaetano Perrotta5 , Paolo Facella5 , Loredana Lopez5 , Marco Pietrella6 , Giulio Gianese7 , Jaroslav Dolezel4 , Giovanni Giuliano6 , Luigi Cattivelli3 , Giorgio Valle1 , A Michele Stanca3
Wheat, one of the worlds most important crops, is characterized by polyploid and large genome. 454 pyrosequencing was used to obtain 2x coverage of the wheat chromosome 5A and the resulting sequence assembly was employed to characterize the content in TEs, genes and miRNAs, as well as to infer the synteny with other grass genomes. Repetitive elements account for 76.13% and 82.23% of the sequence snapshot of the short and long arm, respectively. 276 and 288 known TE families/subfamilies were found on 5AS and 5AL, respectively. The ratio of class I (retroelements) to class II (DNA transposons) was about 7 for both arms. Gene content was determined considering non-redundant reads showing at least one match to an EST or a protein. The results indicated that a coding fraction represents 1.08% and 1.3% of the short and long arm, respectively. 195 candidate miRNA precursors belonging to 16 miRNA families were identified, 92 miRNAs were carried by short arm and 103 miRNAs by long arm. 5A genes were then used to search for syntenic relationships among grass genomes. Short arm was closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; long arm found homologous regions on Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosome 9 and 3. The low coverage sequence of wheat chromosome 5A has provided a description of the main sequence features of this chromosome and new information on transposable elements and their significant contribution to genome size.