Exploring Core Response Mechanisms to Multiple Environmental Stressors Via A Genome-Wide Study in the Brown Alga Saccharina japonica (Laminariales, Phaeophyceae)

Grain protein function prediction based on self-attention mechanism and bidirectional LSTM

With the development of genome sequencing technology, using computing technology to predict grain protein function has become one of the important tasks of bioinformatics. The protein data of four grains, soybean, maize, indica and japonica are selected in this experimental dataset. In this paper, a novel neural network algorithm Chemical-SA-BiLSTM is proposed for grain protein function prediction. The Chemical-SA-BiLSTM algorithm fuses the chemical properties of proteins on the basis of amino acid sequences, and combines the self-attention mechanism with the bidirectional Long Short-Term Memory network. The experimental results show that the Chemical-SA-BiLSTM algorithm is superior to other classical neural network algorithms, and can more accurately predict the protein function, which proves the effectiveness of the Chemical-SA-BiLSTM algorithm in the prediction of grain protein function. The source code of our method is available at https://github.com/HwaTong/Chemical-SA-BiLSTM.

Decreased Salinity Offsets the Stimulation of Elevated pCO2 on Photosynthesis and Synergistically Inhibits the Growth of Juvenile Sporophyte of Saccharina japonica (Laminariaceae, Phaeophyta)

The combined effect of elevated pCO₂ (Partial Pressure of Carbon Dioxide) and decreased salinity, which is mainly caused by freshwater input, on the growth and physiological traits of algae has been poorly assessed. In order to investigate their individual and interactive effects on the development of commercially farmed algae, the juvenile sporophytes of Saccharina japonica were cultivated under different levels of salinity (30, 25 and 20 psu) and pCO₂ (400 and 1000 µatm). Individually, decreased salinity significantly reduced the growth rate and pigments of S. japonica, indicating that the alga was low-salinity stressed. The maximum quantum yield, F_v/F_m, declined at low salinities independent of pCO₂, suggesting that the hyposalinity showed the main effect. Unexpectedly, the higher pCO₂ enhanced the maximum relative electron transport rate (rETR_max) but decreased the growth rate, pigments and soluble carbohydrates contents. This implies a decoupling between the photosynthesis and growth of this alga, which may be linked to an energetic reallocation among the different metabolic processes. Interactively and previously untested, the decreased salinity offset the improvement of rETR_max and aggravated the declines of growth rate and pigment content caused by the elevated pCO₂. These behaviors could be associated with the additionally decreased pH that was induced by the low salinity. Our data, therefore, unveils that the decreased salinity may increase the risks of future CO₂-induced ocean acidification on the production of S. japonica.

Independent Evolution of the MYB Family in Brown Algae

Myeloblastosis (MYB) proteins represent one of the largest families of eukaryotic transcription factors and regulate important processes in growth and development. Studies on MYBs have mainly focused on animals and plants; however, comprehensive analysis across other supergroups such as SAR (stramenopiles, alveolates, and rhizarians) is lacking. This study characterized the structure, evolution, and expression of MYBs in four brown algae, which comprise the biggest multicellular lineage of SAR. Subfamily 1R-MYB comprised heterogeneous proteins, with fewer conserved motifs found outside the MYB domain. Unlike the SHAQKY subgroup of plant 1R-MYB, THAQKY comprised the largest subgroup of brown algal 1R-MYBs. Unlike the expansion of 2R-MYBs in plants, brown algae harbored more 3R-MYBs than 2R-MYBs. At least ten 2R-MYBs, fifteen 3R-MYBs, and one 6R-MYB orthologs existed in the common ancestor of brown algae. Phylogenetic analysis showed that brown algal MYBs had ancient origins and a diverged evolution. They showed strong affinity with stramenopile species, while not with red algae, green algae, or animals, suggesting that brown algal MYBs did not come from the secondary endosymbiosis of red and green plastids. Sequence comparison among all repeats of the three types of MYB subfamilies revealed that the repeat of 1R-MYBs showed higher sequence identity with the R3 of 2R-MYBs and 3R-MYBs, which supports the idea that 1R-MYB was derived from loss of the first and second repeats of the ancestor MYB. Compared with other species of SAR, brown algal MYB proteins exhibited a higher proportion of intrinsic disordered regions, which might contribute to multicellular evolution. Expression analysis showed that many MYB genes are responsive to different stress conditions and developmental stages. The evolution and expression analyses provided a comprehensive analysis of the phylogeny and functions of MYBs in brown algae.