Transcription Factor Analysis of Rhodophytes Suggests Trihelix Transcription Factors Across the Florideophyceae

Transcription factors (TFs) are important gene transcription regulators involved in myriad functions such as development, metabolism, and stress response. TFs are found in all eukaryotes, with many families of TFs unique to plants and algae. Algae are of interest due to a wide range of novel metabolites, of which TFs play an important role in regulating their biosynthesis. In particular, the red algae (phylum Rhodophyta) are a source of several important metabolites that are a current focus of further research. However, to date, investigations of TF families in rhodophytes have been limited due to the relative lack of genomic resources available and the small number of in silico analyses of their TFs. In this study, we used genomic and transcriptomic data to identify rhodophyte TFs. We found that the general proportion of TFs in rhodophytes was overall consistent with previous research. However, for the first time in the rhodophyte class Florideophyceae, we report the presence of a putative TF within the trihelix TF (TTF) family, which are light-sensitive TFs associated with growth and stress response. In particular, we demonstrate evidence suggesting the presence of putative TTFs in three Asparagopsis taxiformis genomes, as well as in several other florideophyte assemblies. This was supported by analyses including Neighbour-Joining phylogeny, protein structure prediction, and motif analysis. In summary, this research reported the repertoire of TFs in rhodophyte algae across a much greater range than previously reported and identified putative TTFs in several algae from the class Florideophyceae. This opens an avenue for further research into the evolution of various TFs in early plants, as well as key regulatory factors in rhodophyte metabolism, though future research, such as functional characterisation, will be required to confirm these findings.