Bioinformatic Analysis of Saffron (Crocus sativus L.) stigma EST sequences to determining functional genome orientation and gene network

Functional genomics methods such as Expressed Sequenced Tag (EST) analysis have provided possibilities for identification, expression analysis and study of transcripts involved in metabolic and regulatory networks. In order to identify of genome orientation and to determine gene networks involved in the evolution of saffron stigma, 6202 EST sequences from mature saffron stigma were analyzed. After initial trimming, sequences clustering and assembling resulted in 910 unigenes (604 Contigs and 304 Singleton). BLAST X revealed that 570 unigene had significant hit among the Arabidopsis protein database, whereas the remaining unigenes displayed no significant match with the any hit. Classifying and gene enrichment analysis of unigenes, put them into 31 distinct functional groups, where 12 groups of them were statistically significant at α=0.01. Gene network of high represented Contigs (which had greater than 20 transcripts), showed that there is a complex gene interaction in mature saffron stigmas. Results revealed that jasmonic acid signalling pathway and its transcription factors such as MYB21 and Zinc fingers play a key role in regulating of stigma primary and secondary metabolism, especially in metabolism of carotenoids (as the most important saffron metabolites). The genes identified in this study could be good candidates for manipulating the evolution and metabolism of saffron stigma.