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

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.

First record of the spatial organization of the nucleosome‐less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)

“…This was in contrast to the other microsatellite motifs analyzed, especially poly C and trimers of CCG, motifs with a 100% CG content and present in high abundance. These results are consistent with the bias toward a higher GC-content of the genomic sequences and transcriptomes of free-living dinoflagellates (Jaeckisch et al 2011, Williams et al 2017. Unlike the genomes of protists, plants, and animals other than green algae, which contain a large proportion of poly-A stretches, in the G. australes genome the predominant mononucleotide is C. There were no differences in the overall abundance of microsatellite motifs with a 33.3% GC-content (e.g., AAC, AAG, or ATC) and those with a 66.6% GCcontent (e.g., ACC, ACG, or AGG) in G. australes.…”

“…2011, Williams et al. 2017). Unlike the genomes of protists, plants, and animals other than green algae, which contain a large proportion of poly‐A stretches, in the G. australes genome the predominant mononucleotide is C. There were no differences in the overall abundance of microsatellite motifs with a 33.3% GC‐content (e.g., AAC, AAG, or ATC) and those with a 66.6% GC‐content (e.g., ACC, ACG, or AGG) in G. australes .…”

An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome

“…To the best of our knowledge, this is the smallest dinoflagellate genome reported so far. The mean GC content of A. ceratii genome was calculated to be 55.9%, which is in the range of published dinoflagellate transcriptomes ( 23 ) but relatively higher compared to Symbiodinium spp. (43.6 to 50.5%) ( 20 – 22 ) and Hematodinium sp.…”

A Global Approach to Estimating the Abundance and Duplication of Polyketide Synthase Domains in Dinoflagellates

“…Davis), Karlodinium veneficum (D. Ballantine), and Akashiwo sanguinea (K. Hirasaka) that were infected with the syndinean parasite of the genus Amoebophyra were collected from previous phylogenetic studies. 1,48,49 For A sanguinea the transcriptome was done with and without infection and for the K. veneficum parasite there is a genome available for comparison. 50 In addition to these transcriptomes the deep sequencing transcriptomes (using Hi-Seq) for K. brevis , 38 and 2 Gambierdiscus species, 51 G. excentricus (S. Fraga), and G. polynesiensis (Chinain and M. Faust) that were assembled using CLC (595M, 118M, 884M reads, respectively) were included.…”