Fuli Liu

Homologous to E6-associated protein Carboxyl Terminus (HECT) is one important family of E3 ubiquitin ligase superfamily involved in the ubiquitin-proteasome pathway. This gene family plays widely roles in the regulation of growth, development and signaling pathways in different organisms, as a specific key molecule in ubiquitin signal transduction. Large number of studies have focused on the identification and characterization of HECT E3 ligase in plants and animals, but studies in Ochrophyta, a phylogenetic lineage that is distantly related to terrestrial plants and animals, are very scarce. This study comprehensively analyzed the HECT E3 ligase gene family in algae Saccharina japonica with significant economic and ecological value. Eighteen HECT E3 ligase members were identified in S. japonica genome, and the physicochemical parameters, phylogenetic relationships, structural mechanisms, functional annotations, and gene expression of these E3 ligases were analyzed and characterized. Additionally, the HECT E3 genes were also identified from other five algae genomes. A total of 90 HECT E3 from the six algae species were used to elucidate the evolutionary relatedness of the HECT gene family in algae. The resulted phylogenetic tree revealed that the HECT family was mainly divided into six branches. Protein structure analysis revealed the conservation of the HECT domain in the entire gene family, showing the substrate binding and structure-function relationships. A large number of regulatory elements involved in stress, hormone regulation, light response, growth and development were identified in the promoter region of SjHECT E3 genes. Expression analysis indicated that members in different SjHECT gene subfamilies might play specific roles in the growth and heat stress response of S. japonica. Overall, the identification and analysis of the HECT E3 gene family in S. japonica laid the foundation for further study on the function and regulatory pathways of HECT in Ochrophyta species.

Saccharina japonica is an ecologically and economically important kelp in cold‐temperate regions. When it is cultivated on a large scale in the temperate and even subtropical zones, heat stress is a frequent abiotic stress. This study is the first attempt to reveal the regulatory mechanism of the response to heat stress from the perspective of DNA methylation in S. japonica. We firstly obtained the characteristics of variation in the methylome under heat stress, and observed that heat stress caused a slight increase in the overall methylation level and methylation rate, especially in the non‐coding regions of the genome. Secondly, we noted that methylation was probably one of factors affecting the expression of genes, and that methylation within the gene body was positively correlated with the gene expression (rho = 0.0784). Moreover, it was found that among the differentially expressed genes regulated by methylation, many genes were related to heat stress response, such as HSP gene family, genes of antioxidant enzymes, genes related to proteasome‐ubiquitination pathway, and plant cell signaling pathways. This study demonstrated that DNA methylation is involved in regulating the response to heat stress, laying a foundation for studying the acclimation and adaptation of S. japonica to heat stress from an epigenetic perspective.

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.

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.