| Title | Analysis of Expressed Sequence Tags from the Red Alga Griffithsia okiensis |
|---|---|
| Author | Hyoungseok Lee1, Hong Kum Lee1, Gynheung An2, and Yoo Kyung Lee1* |
| Address | 1Polar BioCenter, Korea Polar Research Institute (KOPRI), KORDI, Incheon 406-840, Republic of Korea, 2Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea |
| Bibliography | Journal of Microbiology, 45(6),541-546, 2007, |
| DOI | |
| Key Words | codon usage, expressed sequence tags (ESTs), Gene Ontology (GO), Griffithsia okiensis, Porphyra yezoensis, red alga |
| Abstract | Red algae are distributed globally, and the group contains several commercially important species. Griffithsia okiensis is one of the most extensively studied red algal species. In this study, we conducted expressed sequence tag (ESTs) analysis and synonymous codon usage analysis using cultured G. okiensis samples. A total of 1,104 cDNA clones were sequenced using a cDNA library made from samples collected from Dolsan Island, on the southern coast of Korea. The clustering analysis of these sequences allowed for the identification of 1,048 unigene clusters consisting of 36 consensus and 1,012 singleton sequences. BLASTX searches generated 532 significant hits (E-value <10-4) and via further Gene Ontology analysis, we constructed a functional classification of 434 unigenes. Our codon usage analysis showed that unigene clusters with more than three ESTs had higher GC contents (76.5%) at the third position of the codons than the singletons. Also, the majority of the optimal codons of G. okiensis and Chondrus crispus belonging to Bangiophycidae were C-ending, whereas those of Porphyra yezoensis belonging to Florideophycidae were G-ending. An orthologous gene search for the P. yezoensis EST database resulted in the identification of 39 unigenes commonly expressed in two rhodophytes, which have putative functions for structural proteins, protein degradation, signal transduction, stress response, and physiological processes. Although experiments have been conducted on a limited scale, this study provides a material basis for the development of microarrays useful for gene expression studies, as well as useful information for the comparative genomic analysis of red algae. |
| Download PDF | 45(6)_11.pdf |