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virtual unigenes, we compared their sequences against GenBank non redundant protein database with an e value cutoff of 1e 5. The analysis indicated that 20,023 virtual unigenes had significant matches in the nr database, among which 15,126 were cucumber AZ20 genome predicted genes and 4,897 unmappable unigenes, The low percentage of cucumber unmappable unigenes that can be assigned a putative function might be mainly due to the short sequence reads generated TCID by the 454 sequencing technology and the rela tively short sequences of the resulting unigenes, most of which probably lack the conserved func tional domains. Another possible reason is that some of these unigenes might be non coding RNAs.
Gene Ontology terms were further assigned to cucumber virtual unigenes based on their sequence simi larities to known proteins in the UniProt database anno tated with GO terms as well as InterPro and Pfam domains they contain. A total of 15,901 virtual unigenes were assigned at least one GO term, IU1 among which 13,620 were assigned at least one GO term in the biological process category, 13,799 in the molecular func tion category and 12,982 in the cellular component cate gory. These virtual unigenes were further classified into different functional categories using a set of plant spe cific GO slims, which are a list of high level GO terms providing Carcinoid a broad overview of the ontology content, Figure 3 shows the functional classification of cucumber virtual unigenes into plant specific GO slims within the biological process category.
Cellular process, metabolic process, and biosynthetic process were among the most highly represented groups, indicating the flower buds were undergoing rapid growth and extensive metabolic activities. It is worth noting that GO annotations revealed 417 and 129 genes involved in flower development and the pollination process, respectively. Genes involved in other IU1 important biological processes such as stress response, signal transduction, and cell differentiation were also identified through GO annotations. Biochemical pathways To further demonstrate the usefulness of cucumber AZ20 ESTs generated in the present study, we identified biochemical pathways represented by the EST collection. Annotations of cucumber unigenes were fed into the Pathway Tools and this process predicted a total of 343 pathways represented by a total of 5,342 unigenes, which belonged to 1,407 virtual unigenes.
These predicted pathways rep resented the majority of plant biochemical pathways for compound biosynthesis, degradation, utilization, and assimilation, and pathways involved in the processes of detoxification and generation of precursor metabolites and energy. A database containing all the predicted cucumber pathways has been developed and is available through IU1 AZ20 the Cucubit Genomics Database, Enzymes catalyzing almost all steps in several major plant metabolic pathways including Calvin cycle, glycoly sis, gluconeogenesis, pentose phosphate pathway, and several important secondary metabolite biosynthesis pathways including carotenoid biosynthesis and fla vonoid and anthocyanin biosynthesis, could be repre sented by unigenes derived from the cucumber EST collection.
Moreover, genes encoding oxidosqualene cyclase, an enzyme in the cucurbitacin biosynthesis path way, were also found in the EST collection. All these evi dences supported that the ESTs generated under this study provided a valuable resource for cucumber gene discovery and future functional analysis. Comparison of transcriptomes between gynoecious and hermaphroditic flowers Cucumber IU1 is a model system for sex determination stud ies due to its diverse floral sex types, During the past several years, significant progresses have been made in elucidating the mechanisms of plant sex determination, an important and fundamental developmental process of flowering plants, as exemplified by cloning several major sex determining genes in cucurbit species, Despite such advances, little is known about t