A partial expressed sequence tag (EST) library of the economically important red alga Eucheuma denticulatum (N. L. Burham) F. C. Collins and Hervey

Abstract

A library of expressed sequence tags (ESTs) was derived from the economically important Rhodophyta species Eucheuma denticulatum. This small scale EST library represents the first look at the set of genes expressed in any Eucheuma species. A total of 311 clones were analyzed. These 311 sequences clustered into 143 unigenes. Thirty-two of the 143 unigenes showed sufficient similarity to known genes to allow annotation. Of these 32 unigenes, 22 were found in at least one other EST collection from Rhodophyta species. Sixteen of the unigenes showed strong similarity to known genes, with e-values smaller than 1x10-14. Another 16 unigenes could be annotated by relaxing the e-value cut-off to 5x10-4. The identified genes covA ered general metabolic processes (10); translation (2); protein folding, transport, and degradation, including heat shock proteins (6); DNA and RNA binding (2); transcription factors (2); signal transduction, and protein binding (2); cell cycle and apoptosis (2); ion transport (1); and cell membrane, cell wall or extracellular matrix-associated proteins, and other structural proteins (5). Most of the unigenes (111 of them, representing 77.6% of the unigenes), showed no significant similarity to known genes, although 15 of the 111 showed similarity to hypothetical or predicted proteins or raw genomic sequences. Majority of the unannotated unigenes (93 or 64.6% of the library) have not been found in the other Rhodophyta EST libraries, suggesting that many novel genes may still be uncovered by small scale EST collections.