Citation

Cocquyt E., Gile, G.H., Leliaert F., Verbruggen H., Keeling P.J. & De Clerck O. (2010)
Complex phylogenetic distribution of a non-canonical genetic code in green algae
BMC Evolutionary Biology 10: 327

Summary

Background: A non-canonical nuclear genetic code, in which TAG and TAA have been reassigned from stop codons to glutamine, has evolved independently in several eukaryotic lineages, including the ulvophycean green algal orders Dasycladales and Cladophorales. To study the phylogenetic distribution of the standard and noncanonical genetic codes, we generated sequence data of a representative set of ulvophycean green algae and used a robust green algal phylogeny to evaluate different evolutionary scenarios that may account for the origin of the non-canonical code.
Results: This study demonstrates that the Dasycladales and Cladophorales share this alternative genetic code with the related order Trentepohliales and the genus Blastophysa, but not with the Bryopsidales, which is sister to the Dasycladales. This complex phylogenetic distribution whereby all but one representative of a single natural lineage possesses an identical deviant genetic code is unique.
Conclusions: We compare different evolutionary scenarios for the complex phylogenetic distribution of this non-canonical genetic code. A single transition to the noncanonical code followed by a reversal to the canonical code in the Bryopsidales is highly improbable due to the profound genetic changes that coincide with codon reassignment. Multiple independent gains of the non-canonical code, as hypothesized for ciliates, are not very plausible because the same deviant code has evolved in all lineages. Instead we favor a stepwise acquisition model, congruent with the ambiguous intermediate theory, whereby the alternative codes observed in these green algal orders share a single origin. We suggest that the final steps from an ambiguous intermediate situation to a non-canonical code have completed in the Trentepohliales, Dasycladales, Cladophorales and Blastophysa but not in the Bryopsidales. We hypothesize that in the latter lineage an initial stage characterized by translational ambiguity was not followed by final reassignment of both stop codons to glutamine. Instead the standard code was retained by the disappearance of the ambiguously decoding tRNAs from the genome. We correlate the emergence of a non-canonical genetic code in the Ulvophyceae to their multinucleate nature.

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