Analysis of expressed sequence tags (ESTS) from the polar diatom Fragilariopsis cylindrus

Thomas Mock, Andreas Krell, Gernot Glöckner, Üner Kolukisaoglu, Klaus Valentin

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43 Citations (Scopus)

Abstract

Analysis of expressed sequence tags (ESTs) was performed to gain insights into cold adaptation in the polar diatom Fragilariopsis cylindrus Grunow. The EST library was generated from RNA isolated 5 days after F. cylindrus cells were shifted from approximately +5°C to -1.8°C. A total of 1376 ESTs were sequenced from a non-normalized cDNA library and assembled into 996 tentative unique sequences. About 27% of the ESTs displayed similarity (tBLASTX, e-value of =10-4) to predicted proteins in the centric diatom Thalassiosira pseudonana Hasle & Heindal. Eleven additional algae and plant data bases were used for annotation of sequences not covered by Thalassiosira sequences (7%). Most of the ESTs were similar to genes encoding proteins responsible for translation, ribosomal structure, and biogenesis (3%), followed by genes encoding proteins for amino acid transport and metabolism and post-translational modifications. Interestingly, 66% of all the EST sequences from F. cylindrus displayed no similarity (e-value =10-4) to sequences from the 12 non-redundant databases. Even 6 of the 10 strong to moderately expressed sequences in this EST library could not be identified. Adaptation of F. cylindrus to freezing temperatures of seawater may require a complex protein metabolism and possibly also genes, which were highly expressed but still unknown. However, it could also mean that due to low temperatures, there might have been a stronger pressure to adapt amino acid sequences, making it more difficult to identify these unknown sequences and/or that there are still few protist sequences available for comparison.
Original languageEnglish
Pages (from-to)78-85
Number of pages8
JournalJournal of Phycology
Volume42
Issue number1
DOIs
Publication statusPublished - 2006

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