A computational and experimental approach for developing jute ESTs from genomic clones

Gene identification is a leading and essential step in understanding the genome of an organism or for manipulation of genes necessary for incorporating any novel characteristics. However, current technologies and resources are far from shedding light on the genome of organisms like jute for which the whole genome sequence is yet to be determined. An alternative approach for finding genes in such genomes is to find and characterize specific genes, especially those which are differentially expressed under certain conditions. Though expressed sequence tags (ESTs) are widely used for this purpose, generation and characterization of ESTs are not straight forward in many cases. In this situation the available genomic clones can be used to identify and characterize ESTs with the combination of accessible bioinformatics tools such as gene prediction software, NCBI web portal etc and experimental approaches such as RT-PCR followed by sequencing. A number of ESTs for jute have been developed from a previously constructed jute genomic library enriched for simple sequence repeats and also by using the technique of differential display. Some of these ESTs were found to be interesting in terms of their agronomic properties. Keyword: Bioinformatics, RT-PCR, DNA sequencing