title: Computer aided gene mining for gingerol biosynthesis.
abstract: Inspite of the large body of genomic data obtained from the transcriptome of Zingiber officinale, very few studies have focused on the identification and characterization of miRNAs in gingerol biosynthesis. Zingiber officinale transcriptome was analyzed using EST dataset (38169 total) deposited in public domains. In this paper computational functional annotation of the available ESTs and identification of genes which play a significant role in gingerol biosynthesis are described. Zingiber officinale transcriptome was analyzed using EST dataset (38169 total) from ncbi. ESTs were clustered and assembled, resulting in 8624 contigs and 8821 singletons. Assembled dataset was then submitted to the EST functional annotation workflow including blast, gene ontology (go) analysis, and pathway enrichment by kyoto encyclopedia of genes and genomes (kegg) and interproscan. The unigene datasets were further exploited to identify simple sequence repeats that enable linkage mapping. A total of 409 simple sequence repeats were identified from the contigs. Furthermore we examined the existence of novel miRNAs from the ESTs in rhizome, root and leaf tissues. EST analysis revealed the presence of single hypothetical miRNA in rhizome tissue. The hypothetical miRNA is warranted to play an important role in controlling genes involved in gingerol biosynthesis and hence demands experimental validation. The assembly and associated information of transcriptome data provides a comprehensive functional and evolutionary characterization of genomics of Zingiber officinale. As an effort to make the genomic and transcriptomic data widely available to the public domain, the results were integrated into a web-based Ginger EST database which is freely accessible at http://www.kaubic.in/gingerest/.
authors.affiliation: Bioinformatics Centre (DIC), College of Horticulture, Kerala Agricultural University, Vellanikkara, 680 656, Thrissur, Kerala, India.
authors.forename: Priyanka
authors.initials: P
authors.lastname: James
authors.affiliation: Bioinformatics Centre (DIC), College of Horticulture, Kerala Agricultural University, Vellanikkara, 680 656, Thrissur, Kerala, India.
authors.forename: Bincy
authors.initials: B
authors.lastname: Baby
authors.affiliation: Bioinformatics Centre (DIC), College of Horticulture, Kerala Agricultural University, Vellanikkara, 680 656, Thrissur, Kerala, India.
authors.forename: SonaSona
authors.initials: S
authors.lastname: Charles
authors.affiliation: Bioinformatics Centre (DIC), College of Horticulture, Kerala Agricultural University, Vellanikkara, 680 656, Thrissur, Kerala, India.
authors.forename: Lekshmysree Saraschandran
authors.initials: LS
authors.lastname: Nair
authors.affiliation: Bioinformatics Centre (DIC), College of Horticulture, Kerala Agricultural University, Vellanikkara, 680 656, Thrissur, Kerala, India.
authors.forename: Puthiyaveetil Abdulla
authors.initials: PA
authors.lastname: Nazeem
keywords: ESTs; gingerol biosynthesis; miRNAs; transcriptomics