Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA

First Survey Of The Wheat Chromosome 5A Composition Through A Next Generation Sequencing Approach

Nicola Vitulo¹ , Alessandro Albiero^1,2 , 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

¹  CRIBI Biotechnology Center, University of Padova via U. Bassi, 58/b, 35131 Padova – Italy.

²  Bmr-genomics srl via Redipuglia 21/A, 35131 Padova – Italy.

³  CRA Genomics Research Centre, via S.Protaso 302, I-29017 Fiorenzuola d’Arda (Pc), Italy.

⁴  Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic.

⁵  ENEA, TRISAIA Research Center, S.S. 106 Ionica, 75026 Rotondella (Matera), Italy.

⁶  ENEA, CASACCIA Research Center, via Anguillarese 301, 00123 Rome, Italy.

⁷  Ylichron Srl, via Anguillarese 301, 00123 Rome, Italy.

Wheat, one of the world’s 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.