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

Mock, T, Krell, A, Glockner, G, Kolukisaoglu, U and Valentin, K (2006) Analysis of expressed sequence tags (ESTS) from the polar diatom Fragilariopsis cylindrus. Journal of Phycology, 42 (1). pp. 78-85. ISSN 0022-3646

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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.

Item Type: Article
Faculty \ School: Faculty of Science > School of Environmental Sciences
University of East Anglia > Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
University of East Anglia > Faculty of Science > Research Groups > Environmental Biology
University of East Anglia > Faculty of Science > Research Groups > Resources, Sustainability and Governance
University of East Anglia > Faculty of Science > Research Groups > Marine and Atmospheric Sciences
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Depositing User: Rosie Cullington
Date Deposited: 30 Jun 2011 16:17
Last Modified: 10 Sep 2018 15:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/33135
DOI: 10.1111/j.1529-8817.2006.00164.x

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