Description: Macroalgal (seaweed) genomic resources are generally lacking as compared to other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.

Description: Climate change is significantly impacting the structure and function of marine ecosystems world wide with implications for species distribution ranges. In coastal systems, climate change may also alter other abiotic factors such as salinity, which may decrease due increased glacial melting in the Arctic or precipitation in temperate regions. Despite the prime ecological importance of kelps (order Laminariales) which dominate rocky benthic ecosystems in temperate to polar regions, the acclimation mechanisms and transcriptomic responses remain understudied. Here, we investigate the physiological and transcriptomic responses in sporophytes of the sugar kelp, Saccharina latissima to salinity stress after acclimation to temperature and their nterrelationships. Juvenile sporophytes of a strain from Roscoff, France were pre-cultivated at 8°C and 30 PSU for three months. After seven days of acclimation to 0°C and 15°C, sporophytes were exposed to a low salinity treatment (20 PSU) for 24 h. We established a reference transcriptome from all reads obtained through Illumina HiSeq. A total of 205 363 transcripts were assembled containing 135 959 “Trinity’s genes”. Gene expression is mostly driven by salinity stress than by temperature. The highest number of regulated genes, in comparison to the control, was found in response to the treatment 0°C low salinity (3003), followed by 8°C low salinity (1491) and 15°C low salinity (1158). Moreover, only few genes (168) were found to be differentially expressed in all low salinity treatments, showing that the response to low salinity is modulated by temperature. Growth, photosynthetic efficiency and pigment content were also impacted by stress.

Description: The Arctic region is currently facing substantial environmental changes due to global warming. Melting glaciers cause reduced salinity environments in coastal Arctic habitats, which may be stressful for kelp beds. To investigate the responses of the kelp Saccharina latissima to the warming Arctic, we studied the transcriptomic changes of S. latissima from Kongsfjorden (Svalbard, Norway) over a 24-hour exposure to two salinities (Absolute Salinity [SA] 20 and 30) after a 7-day pre-acclimation at three temperatures (0, 8 and 15∘C). In addition, corresponding physiological data were assessed during an 11-days salinity/temperature experiment. Growth and maximal quantum yield for photosystem II fluorescence were positively affected by increased temperature during acclimation, whereas hyposalinity caused negative effects at the last day of treatment. In contrast, hyposalinity induced marked changes on the transcriptomic level. Compared to the control (8∘C – SA 30), the 8∘C – SA 20 exhibited the highest number of differentially expressed genes (DEGs), followed by the 0∘C – SA 20. Comparisons indicate that S. latissima tends to convert its energy from primary metabolism (e.g. photosynthesis) to antioxidant activity under hyposaline stress. The increase in physiological performance at 15∘C shows that S. latissima in the Arctic region can adjust and might even benefit from increased temperatures. However, in Arctic fjord environments its performance might become impaired by decreased salinity as a result of ice melting.

Description: Background: Kelps (Laminariales, Phaeophyceae) are brown macroalgae of utmost ecological, and increasingly economic, importance on temperate to polar rocky shores. Omics approaches in brown algae are still scarce and knowledge of their acclimation mechanisms to the changing conditions experienced in coastal environments can benefit from the application of RNA-sequencing. Despite evidence of ecotypic differentiation, transcriptomic responses from distinct geographical locations have, to our knowledge, never been studied in the sugar kelp Saccharina latissima so far. Results: In this study we investigated gene expression responses using RNA-sequencing of S. latissima from environments with contrasting temperature and salinity conditions – Roscoff, in temperate eastern Atlantic, and Spitsbergen in the Arctic. Juvenile sporophytes derived from uniparental stock cultures from both locations were pre-cultivated at 8 °C and SA 30. Sporophytes acclimated to 0 °C, 8 °C and 15 °C were exposed to a low salinity treatment (SA 20) for 24 h. Hyposalinity had a greater impact at the transcriptomic level than the temperature alone, and its effects were modulated by temperature. Namely, photosynthesis and pigment synthesis were extensively repressed by low salinity at low temperatures. Although some responses were shared among sporophytes from the different sites, marked differences were revealed by principal component analysis, differential expression and GO enrichment. The interaction between low temperature and low salinity drove the largest changes in gene expression in sporophytes from Roscoff while specimens from Spitsbergen required more metabolic adjustment at higher temperatures. Moreover, genes related to cell wall adjustment were differentially expressed between Spitsbergen and Roscoff control samples. Conclusions: Our study reveals interactive effects of temperature and salinity on transcriptomic profiles in S. latissima. Moreover, our data suggest that under identical culture conditions sporophytes from different locations diverge in their transcriptomic responses. This is probably connected to variations in temperature and salinity in their respective environment of origin. The current transcriptomic results support the plastic response pattern in sugar kelp which is a species with several reported ecotypes. Our data provide the baseline for a better understanding of the underlying processes of physiological plasticity and may help in the future to identify strains adapted to specific environments and its genetic control.

Description: The Arctic region is currently facing substantial environmental changes. Melting of glaciers as a consequence of increasing temperature subsequently creates stressful environmental conditions, such as reduced salinity in coastal habitats of kelp beds. We investigated the physiological and transcriptomic performance of the sugar kelp Saccharina latissima from Kongsfjorden (Svalbard, Norway) over a 24-hour exposure at two salinities (20 and 30 psu) after a 7- day pre-acclimation at three temperatures (0, 8 and 15°C). The results demonstrate that the maximum quantum yield of PS II (Fv/Fm) at 15° C was significantly higher than at 0° C, but showed no difference at the two salinities. Pigment content exhibited similar response patterns. Salinity, however, affected gene expression much stronger than temperature. The highest number of differentially expressed genes (DEGs;-DESeq2 with log2Ratio≥2), compared to the control at 8°C and normal salinity, was found in the specimens at 8°C and low salinity (1,374), followed by samples at 0°C and low salinity (1,193). The lowest number of DEGs appeared in the individuals at 0°C and normal salinity (274). Expression profile changes mainly focused on regulations of photosynthetic components and transport processes, as well as induction of ROS scavengers. On the physiological level, our findings indicate a high plastic performance of S. latissima at higher temperatures and lower salinities accompanied by significant gene expression modulation

Description: Saccharina latissima is an economically and ecologically relevant kelp species in Europe and North America. In kelps, the sexuality is expressed during the haploid life stage and the microscopic gametophytes exhibit significant sexual dimorphism. To understand the sex-dependent impact of temperature on the gametophyte stage, we analyzed for the first time, gene expression profiles of male and female gametophytes at three different temperatures (4, 12, and 20°C) characteristic for the species distribution range by using RNA-sequencing. We identified several differentially expressed genes (DEGs) between sexes; while female biased genes were enriched in general metabolism and energy production, male biased genes function within cell cycle and signaling. In our study, temperature modulated sex-biased gene expression, with only a small percentage of DEGs consistently male (7%) or female-biased (12%) at the three temperatures. Female gametophytes responded stronger to higher temperatures than males, suggesting that males are more heat tolerant. Differences between S. latissima and other brown algal gender-dependent gene expression might mirror the different evolutionary and ecological contexts. Genomic information on kelp gametophyte is still scarce and thus this study adds to our knowledge on sex differences in abiotic stress responses in macroalgae at the transcriptomic level.

Description: 〈jats:p〉Kelps in the Arctic region are facing challenging natural conditions. They experience over 120 days of darkness during the polar night surviving on storage compounds without conducting photosynthesis. Furthermore, the Arctic is experiencing continuous warming as a consequence of climate change. Such temperature increase may enhance the metabolic activity of kelps, using up storage compounds faster. As the survival strategy of kelps during darkness in the warming Arctic is poorly understood, we studied the physiological and transcriptomic responses of 〈jats:italic〉Saccharina latissima〈/jats:italic〉, one of the most common kelp species in the Arctic, after a 2-week dark exposure at two temperatures (0 and 4°C) versus the same temperatures under low light conditions. Growth rates were decreased in darkness but remained stable at two temperatures. Pigments had higher values in darkness and at 4°C. Darkness had a greater impact on the transcriptomic performance of 〈jats:italic〉S. latissima〈/jats:italic〉 than increased temperature according to the high numbers of differentially expressed genes between dark and light treatments. Darkness generally repressed the expression of genes coding for glycolysis and metabolite biosynthesis, as well as some energy-demanding processes, such as synthesis of photosynthetic components and transporters. Moreover, increased temperature enhanced these repressions, while the expression of some genes encoding components of the lipid and laminaran catabolism, glyoxylate cycle and signaling were enhanced in darkness. Our study helps to understand the survival strategy of kelp in the early polar night and its potential resilience to the warming Arctic.〈/jats:p〉

Description: Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.