Gene identification in Phytophthora capsici through expressed sequence tags

Abstract

Expressed Sequence Tags (ESTs) are a rich source of information for gene discovery. In this paper, we describe the annotation of ESTs of Phytophthora capsici whose complete genome is not yet available. P. capsici is an Oomycete plant pathogen capable of infecting wide range of plants including cucumber, squash, melons, pumpkin, pepper, tomato and eggplant. In India it causes severe economic losses in black pepper, chillies and cocoa. Towards the understanding of gene function in P. capsici, we undertook the functional annotation of ESTs available at NCBI. A total of 56,457 ESTs were downloaded from NCBI and assembled into 5966 contigs. Functional categorization of these ESTs was performed using database similarity search. By functional analysis, we estimated that 84.73% of transcripts encode significant proteins. The most prominent sequences corresponds to members of metabolic pathways, avirulence-associated protein, beta-tubulin, calcium/calmodulin dependent protein kinase 3, catalase, endo-1, 4-betaglucanase, cyst germination specific acidic repeat protein precursor, elicitin-like protein, glucanase inhibitor protein, heat shock protein, Kazal-like serine protease inhibitor, mitogen-activated protein kinase, ribosomal protein, serine/threonine kinase, syntaxin and ubiquitin. This EST-gene discovery information can be used to design sequence specific markers for P. capsici identification.