Abstract
Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is known about it in phytoplankton. This phenomenon is thought to be driven by selection for translational efficiency. As the efficacy of selection is proportional to the effective population size, species with large population sizes, such as phytoplankton, are expected to have strong codon bias. To test this, we measured codon bias in 215 strains from Haptophyta, Chlorophyta, Ochrophyta (except diatoms that were studied previously), Dinophyta, Cryptophyta, Ciliophora, unicellular Rhodophyta and Chlorarachniophyta. Codon bias is modest in most groups, despite the astronomically large population sizes of marine phytoplankton. The strength of the codon bias, measured with the effective number of codons, is the strongest in Haptophyta and the weakest in Chlorarachniophyta. The optimal codons are GC-ending in most cases, but several shifts to AT-ending codons were observed (mainly in Ochrophyta and Ciliophora). As it takes a long time to reach a new equilibrium after such shifts, species having AT-ending codons show a lower frequency of optimal codons compared to other species. Genetic diversity, calculated for species with more than three strains sequenced, is modest, indicating that the effective population sizes are many orders of magnitude lower than the astronomically large census population sizes, which helps to explain the modest codon bias in marine phytoplankton. This study represents the first comparative analysis of codon bias across multiple major phytoplankton groups.
Highlights
Codon usage bias (CUB)—the preferential use of one of the synonymous codons encoding the same amino acid—is an important feature of pro- and eukaryotic genomes [1,2]
This significantly expands the work on phytoplankton CUB, which was previously limited to diatoms [8] and Mamiellophyceae [7]
Codon bias was relatively modest in all groups, with the strongest overall CUB observed in Haptophyta, which was stronger than previously observed in diatoms but comparable to the CUB in terrestrial macro-organisms with large population sizes, such as Drosophila [30]
Summary
Codon usage bias (CUB)—the preferential use of one of the synonymous codons encoding the same amino acid—is an important feature of pro- and eukaryotic genomes [1,2] This bias is known in many species of bacteria [3,4], plants [5], insects [6], green algae [7] and diatoms [8] and appears to be universal. It has not yet been systematically characterised across a wide range of phytoplankton groups. The aim of this paper is to characterise and compare CUB across a wide diversity of phytoplankton groups
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