Model

Saccharina latissima
Saccharina latissima (L.) C.E. Lane, C. Mayes, Druehl, et G. W. Saunders is a species of Laminariales that has a wide latitudinal range in the Northern hemisphere from polar to temperate waters. In the eastern Atlantic, it is distributed from the Arctic (>80°N) to the north of Portugal (41.5° N) and from the lowermost intertidal to 30 meters depth. This suggests that the species has a high potential to adapt to variations in temperature and irradiance.

Scientific Team

Project leaders are Catia Monteiro, Kai Bischof from Bremen university and Jonas Collen from LBI2M ROSCOFF.

Project collaborator are Sandra Heinrich, (University of Hamburg), Inka Bartsch and Klaus Ulrich Valentin (AWI Bremerhaven), Gernot Glöckner (University of Cologne)

Bioinformatic analysis was conducted by Lars Harms (AWI Bremerhaven) and Erwan Corre ABiMS plateform

Scientific Context

Kelps (Laminariales, Phaeophyceae) are brown macroalgae of utmost ecological, and increasingly economic, importance in 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.

Bioinformatic analysis

Raw reads were quality controlled by FastQC v. 0.11.5 and quality filtered using Trimmomatic v. 0.36. Quality filtering was performed using the following parameters: leading 3, trailing 3, sliding window 4:15, minlen 30. The transcriptome of the sporophytes was assembled based on reads from sporophytes raised from spores collected in Roscoff, France and the gametophyte transcriptome based on reads from gametophytes raised from spores collected in Helgoland, Germany. The assemblies were performed with Trinity v 2.4.0 including the reads normalization step corresponding to the Trinity implementation of the diginorm method. The assembler was run with default parameters. The quality of the transcriptome assemblies was evaluated by using BUSCO v2.0 with eukaryote dataset (OrthoDB v9.1]. To check for potential contamination, bacterial and oomycete sequences obtained from Genbank were compared to the transcriptome assembly by sequence similarity search (blastn). Functional annotation was performed using the Trinotate functional annotation pipeline with the UniRef90 database as additional reference (all databases up to date in October 2017).

Publications

Huiru Li, Cátia Monteiro, Sandra Heinrich, Inka Bartsch, Klaus Valentin, Lars Harms, Gernot Glöckner, Erwan Corre, and Kai Bischof. "Responses of the kelp Saccharina latissima (Phaeophyceae) to the warming Arctic: from physiology to transcriptomics." Physiologia plantarum (2019). doi:10.1111/ppl.13009 https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.13009
Cátia Monteiro, Sandra Heinrich, Inka Bartsch, Klaus Valentin, Erwan Corre, Jonas Collén, Lars Harms, Gernot Glöckner and Kai Bischof .“Temperature dependent sex-biased gene expression in the gametophytes of the kelp Saccharina latissima” preprint available on https://www.biorxiv.org/content/10.1101/750455v1

Funding

This work was supported by the German Research Foundation for funding within the ERA-Net Cofund BiodivERsA 3 program MARFOR (ANR-16-EBI3-0005-01). Further funding was provided by the MARES Joint Doctoral Programme on Marine Ecosystem Health & Conservation funded through Erasmus Mundus (grant number MARES_14_09) and by the Alfred-Wegener-Institute Helmholtz- Centre for Polar and Marine Research (Bremerhaven, Germany).