Houde, Mario and Belcaid, Mahdi and Ouellet, François and Danyluk, Jean and Monroy, Antonio F and Dryanova, Ani and Gulick, Patrick and Bergeron, Anne and Laroche, André and Links, Matthew G and MacCarthy, Luke and Crosby, William L and Sarhan, Fathey (2006) Wheat EST resources for functional genomics of abiotic stress. BMC Genomics, 7 (1). p. 149. ISSN 14712164
Official URL: http://dx.doi.org/10.1186/1471-2164-7-149
Background: Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project.
Results :We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology.
Conclusion: We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals.
|Divisions:||Concordia University > Faculty of Arts and Science > Biology|
|Authors:||Houde, Mario and Belcaid, Mahdi and Ouellet, François and Danyluk, Jean and Monroy, Antonio F and Dryanova, Ani and Gulick, Patrick and Bergeron, Anne and Laroche, André and Links, Matthew G and MacCarthy, Luke and Crosby, William L and Sarhan, Fathey|
|Journal or Publication:||BMC Genomics|
|Digital Object Identifier (DOI):||10.1186/1471-2164-7-149|
|Deposited By:||ANDREA MURRAY|
|Deposited On:||28 Nov 2011 19:54|
|Last Modified:||05 Nov 2016 01:46|
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