Analysis of expressed sequence tags from cDNA library of Fusarium culmorum infected barley (Hordeum vulgare L.) roots



Feyza Tufan1, Cüneyt Uçarlı1 & Filiz Gürel1, 2*



1Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, 34134 Vezneciler, Istanbul, Turkey; 2Istanbul University, Research and Application Center for Biotechnology and Genetic Engineering, 34134 Vezneciler, Istanbul, Turkey


Email; *Corresponding author


Article Type




Received January 09, 2015; Accepted January 10, 2015; Published January 30, 2015



Fusarium culmorum is one of the most common and globally important causal agent of root and crown rot diseases of cereals. These diseases cause grain yield loss and reduced grain quality in barley. In this study, we have analyzed an expressed sequence tag (EST) database derived from F. culmorum infected barley root tissues available at the National Center for Biotechnology Information (NCBI). The 2294 sequences were assembled into 1619 non-redundant sequences consisting of 359 contigs and 1260 singletons using the program CAP3. BLASTX analysis for these sequences was conducted in order to find similar sequences in all databases. Gene Ontology search, enzyme search, KEGG mapping and InterProScan search were done using Blast2GO 3.0.7 tool. By BLASTX analysis, 41.7%, 7.7%, 3.2% and 47.4% of ESTs were categorized as annotated, unannotated, not mapping and without blast hits, respectively. BLASTX analysis revealed that the majority of top hits were barley proteins (43.5%). Based on Gene Ontology classification, 38.3%, 31.3%, and 16% of ESTs were assigned to molecular function, biological process, and cellular component GO terms, respectively. Most abundant GO terms were as follows: 157 sequences were related to response to stress (biological process), 207 sequences were related to ion binding (molecular function), and 160 sequences were related to plastid (cellular component). Furthermore, based on KEGG mapping, 369 sequences could be assigned to 264 enzymes and 83 different KEGG pathways. According to Enzyme Commission (EC) distribution; 94 sequences were transferases (EC2) while 70 sequences were hydrolases (EC3).



barley, ESTs, root rot and crown rot diseases, Fusarium culmorum



Tufan et al. Bioinformation 11(1): 034-038 (2015)

Edited by

P Kangueane






Biomedical Informatics



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