Characterization of 475 expressed sequence tags generated from root cDNA clones of Brassica napus by single-pass sequencing

Abstract

As a part of our efforts to provide a molecular genetic resource of Brassica plants, we have generated 475 expressed sequence tags (ESTs) from randomly selected 412 root cDNA clones of Brassica napus. These ESTs were generated from two types of cDNA library; one primed with oligo(dT) but with partial deletions from the ends of the cDNA molecules and the other primed with random hexamer. Of the 412 clones, 333 clones (79.3%) provided non-redundant ESTs. A similarity search of these ESTs against the NCBI non-redundant protein database revealed that 139 ESTs (29.3%) are significantly similar to the protein coding sequences in the database. These include 42 ESTs related to the genes from other kingdoms, showing that the EST approach is effective in identifying previously unknown plant genes in a large scale. Functional categorization of the database-matched ESTs showed that defense- or stress-related genes as well as genes involved in the primary metabolic pathways and in translation of mRNAs are most abundantly represented. We also discuss the comparison analysis of the characteristics of the ESTs generated from the different types of cDNA library.