Aureochrome (AUREO) is a kind of blue light photoreceptor with both LOV and bZIP structural domains, identified only in Stramenopiles. It functions as a transcription factor that responds to blue light, playing diverse roles in the growth, development, and reproduction of Stramenopiles. Most of its functions are currently unknown, especially in the economically important alga S. japonica farmed on a large scale. This study provided a comprehensive analysis of the characteristics of AUREO gene families in seven algae, focusing on the AUREOs of S. japonica. AUREO genes were strictly identified from seven algal genomes. Then AUREO phylogenetic tree was constructed from 44 conserved AUREO genes collected. These AUREO genes were divided into five groups based on phylogenetic relationships. A total of 28 genes unnamed previously were named according to the phylogenetic tree. A large number of different cis-acting elements, especially bZIP transcription factors, were discovered upstream of AUREO genes in brown algae. Different intron/exon structural patterns were identified among all AUREOs. Transcriptomic data indicated that the expression of Sj AUREO varied significantly during the different development stages of S. japonica gametophytes. Periodic rhythms of light induction experiments indicate that Sj AUREO existed in a light-dependent circadian expression pattern, differing from other similar studies in the past. This may indicate that blue light affects gametophyte development through AUREO as a light signal receptor. This study systematically identified and analyzed the AUREO gene family in seven representative brown algae, which lay a good foundation for further study and understanding of AUERO functions in agal growth and development.

Cryptochrome/Photolyase Family (CPF) is a widely distributed and highly conserved gene family. The CPF includes photolyases that repair UV-induced DNA damage and blue-light receptors cryptochromes that are known for their photoreceptive functions in terrestrial plants. This study mainly emphasized the CPF members of the economically important brown alga Saccharina japonica, and traces the evolutionary relationship and distribution of this family in algae. Eight new CPF members were identified from the genomes of S. japonica and Undaria pinnatifida, and sixty CPF members from other different species were collected simultaneously for the phylogenetic analysis. Phylogenetic and transcriptional analyses provide evidence for the evolution and function of CPF genes in brown algae. According to the phylogenetic tree, the CPF family was divided into five branches. Photolyase homology domain (PHR) and a non-covalently bound flavin adenine dinucleotide (FAD) molecule are present in the CPF members of two brown algae S. japonica and U. pinnatifida. But they lack the typical C-terminal extension (CCT) characteristic of plant-like cryptochromes. The brown algae Ectocarpus siliculosus and U. pinnatifida have both animal-like CPF and plant-like CPF while only plant CPF members were identified in S. japonica. The results of RNA-seq and qPCR indicated that Sj Cryptochrome-DASH1 (CRY-DASH1) and Sj cyclobutane pyrimidine dimer (CPD) genes may not only play a role in light response but also play an important role in the gametophyte development of S. japonica. Protein interaction network of Sj CPF members showed that there are circadian clock protein Timeless homologous genes in S. japonica, which are located in the core position of the protein interaction network. This implied that Sj CPF members may transmit information by interacting with downstream Timeless genes. These results provide information for subsequent research on functional and regulatory pathways of CPFs in algae species.