Genomics analyses in kelp species

Kelps are large brown algae in the order Laminariales. Kelp species have different distribution ranges along temperate to Polar rocky coastal lines. We sequenced DNA from three Laminaria species namely Laminaria digitata, Laminaria solidungula and Laminaria rodriguezii. Laminaria digitata is found in the Northern Atlantic region with a southern boundary in Brittany (France) or Massachusetts (USA) and a northern boundary in the Artic. Laminaria solidungula is endemic to the Artic and Laminaria rodriguezii is restricted to deep waters of Mediterranean Sea. Currently, not much is known about the nuclear and organellar genomes of kelp species. To initiate the analysis of sequencing data in kelp species the organellar genomes of Laminaria species were generated. The mitochondrial and chloroplast genomes of Laminaria rodriguezii and Laminaria solidungula, and chloroplast genome of Laminaria digitata were analysed and compared with phylogenetic trees derived from publicly available complete mitochondrial and chloroplast kelp genomes. All analysed kelp organellar genomes were found collinear, where large insertion, deletion (indels) or rearrangements were rare with some essential exceptions. Laminaria rodriguezii is very closely related to the North Atlantic temperate to Arctic Laminaria digitata according to the chloroplast and mitochondrial phylogeny. In the mitochondrial genome of Laminaria rodriguezii a stretch of more than 700 base pairs was found, which was not present in any other kelp sequenced so far. The translated Open Reading Frame (ORF) matches a protein coding region in the mitochondrial genome from Desmarestia viridis, a brown seaweed with a cold-temperate to Arctic distribution in the order Desmarestiales, which is closely related to the Laminariales. The high similarity of overlapping parts of two ORFs suggests that it originated through independent introduction, potentially by infection with similar mitoviruses, which is currently known in fungi and plants only. In the chloroplast genomes of Laminaria solidungula a small rearrangement at the inverted repeat regions was found. These rearrangements led to the pseudogenisation of ycf37 gene in Laminaria solidungula, a gene possibly required under high light conditions. This defunct gene might be one of the reasons why the habitat ranges of Laminaria solidungula is restricted to lowlight sublittoral sites in the incomplete lineage sorting of chloroplast genomes in kelp species. This work laid the foundation for analysis of nuclear genome (ca. 400Mb) of Laminaria digitata. The Single nucleotide polymorphism analysis yielded a first glimpse into the population diversity of this species. The draft genome analysis of Laminaria digitata will be part of the comprehensive analysis of brown algal genomes in the framework of the international Phaeoexplorer project led by the Biologigue de Roscoff in France.