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Functional characterization of luciferase in a brittle star indicates parallel evolution influenced by genomic availability of haloalkane dehalogenase

Lau, Emily1; Majerová, Marika2; Hensley, Nicholai3; Mukherjee, Arnab1; Vasina, Michal2; Pluskal, Daniel2; Damborsky, Jiri2; Prokop, Zbynek2; Delroisse, Jérôme4; Bayaert, Wendy-Shirley4; Parey, Elise5; Oliveri, Paola5; Marletaz, Ferdinand5; Marek, Martin2; Oakley, Todd1

Published May 13, 2025 on Dryad. https://doi.org/10.5061/dryad.rv15dv4gm

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May 13, 2025 version files 2.78 MB

Abstract

Determining why convergent traits use distinct versus shared genetic components is crucial for understanding how evolutionary processes generate and sustain biodiversity. However, the factors dictating the genetic underpinnings of convergent traits remain incompletely understood. Here, we use heterologous protein expression, biochemical assays, and phylogenetic analyses to confirm the origin of a luciferase gene from haloalkane dehalogenases in the brittle star Amphiura filiformis. Through database searches and gene tree analyses, we also show a complex pattern of presence and absence of haloalkane dehalogenases across organismal genomes. These results first confirm parallel evolution across a vast phylogenetic distance, because octocorals like Renilla also use luciferase derived from haloalkane dehalogenases. This parallel evolution is surprising, even though previously hypothesized, because many organisms that also use coelenterazine as the bioluminescence substrate evolved completely distinct luciferases. The inability to detect haloalkane dehalogenases in the genomes of several bioluminescent groups suggests that the distribution of this gene family influences its recruitment as a luciferase. Together, our findings highlight how biochemical function and genomic availability help determine whether distinct or shared genetic components are used during the convergent evolution of traits like bioluminescence.