Transcriptome analysis of core dinoflagellates reveals a universal bias towards "GC" rich codons
MetadataShow full item record
AbstractAlthough 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. Copyright 2017 by the authors.
SponsorsThis work was funded by a grant from Oceans and Human Health NIH R01ES021949-01/NSF OCE1313888 to Allen Place and Rosemary Jagus. The authors would like to gratefully acknowledge the contributions of Deaundrae Howard, an undergraduate research intern from Morgan State University.
Identifier to cite or link to this itemhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85019620164&doi=10.3390%2fmd15050125&partnerID=40&md5=e95998c990ff0c2dd01680d5ca3d0ce3; http://hdl.handle.net/10713/11101
- A general model of codon bias due to GC mutational bias.
- Authors: Palidwor GA, Perkins TJ, Xia X
- Issue date: 2010 Oct 27
- Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome.
- Authors: Choudhury MN, Uddin A, Chakraborty S
- Issue date: 2017 Jun
- [Analysis of codon usage bias based on Fritillaria cirrhosa transcriptome].
- Authors: Li Y, Kuang XJ, Sun C, Chen SL
- Issue date: 2016 Jun
- CodonO: codon usage bias analysis within and across genomes.
- Authors: Angellotti MC, Bhuiyan SB, Chen G, Wan XF
- Issue date: 2007 Jul
- Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences.
- Authors: Singh ND, Arndt PF, Petrov DA
- Issue date: 2006 Oct 18