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Mar. Drugs 2017, 15(5), 125; doi:10.3390/md15050125

Transcriptome Analysis of Core Dinoflagellates Reveals a Universal Bias towards “GC” Rich Codons

Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt St., Baltimore, MD 21202, USA
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Academic Editor: Paul Long
Received: 7 March 2017 / Revised: 11 April 2017 / Accepted: 20 April 2017 / Published: 27 April 2017
(This article belongs to the Special Issue Advances and New Perspectives in Marine Biotechnology II 2016)
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Abstract

Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-documented mechanism for controlling gene expression during translation is codon bias, whereby specific codons slow or even terminate protein synthesis. Approximately 10,000 annotatable genes from fifteen “core” dinoflagellate transcriptomes along a range of overall guanine and cytosine (GC) content were used for codonW analysis to determine the relative synonymous codon usage (RSCU) and the GC content at each codon position. GC bias in the analyzed dataset and at the third codon position varied from 51% and 54% to 66% and 88%, respectively. Codons poor in GC were observed to be universally absent, but bias was most pronounced for codons ending in uracil followed by adenine (UA). GC bias at the third codon position was able to explain low abundance codons as well as the low effective number of codons. Thus, we propose that a bias towards codons rich in GC bases is a universal feature of core dinoflagellates, possibly relating to their unique chromosome structure, and not likely a major mechanism for controlling gene expression. View Full-Text
Keywords: dinoflagellate; toxin; codon bias; gene expression dinoflagellate; toxin; codon bias; gene expression
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Williams, E.; Place, A.; Bachvaroff, T. Transcriptome Analysis of Core Dinoflagellates Reveals a Universal Bias towards “GC” Rich Codons. Mar. Drugs 2017, 15, 125.

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