Abstract
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).
Highlights
One of the most common and globally important problems of cereal breeding is Fusarium root rot (FRR) and Fusarium crown rot (FCR) diseases [1,2,3]
Results & Discussion: Analysis of expressed sequence tag (EST) libraries A total of 2306 ESTs, 1168 and 1138 from LIBEST_016901 and LIBEST_016904 were downloaded in FASTA format
The trimmed 2294 ESTs were assembled into clusters by means of CAP3 program. 1034 ESTs were grouped into 359 contigs and 1260 ESTs represented singletons
Summary
One of the most common and globally important problems of cereal breeding is Fusarium root rot (FRR) and Fusarium crown rot (FCR) diseases [1,2,3]. In the development of these diseases, a fungi complex consisting of Fusarium culmorum, Fusarium pseudograminearum (Syn: Fusarium graminearum), Microdochium nivale (Syn: Fusarium nivale), Fusarium avenaceum, Fusarium acuminatum, Bipolaris sorokiniana, Gaeumannomyces graminis and other species plays a major role [4]. The surveys carried out in Turkey showed that F. culmorum was the most abundant among these fungi [5]. In order to reduce the use of pesticide in farming and struggling with the disease, it is crucial to investigate the mechanisms of natural resistance [6]. Investigation of resistance at the molecular level involves mapping of quantitative trait loci [7] and identification of resistance genes [8]. Induction of genes from several pathways after pathogen infection strongly indicates their relation to the plant defense system [9]
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