Description: Macroalgae of the order Laminariales (kelps) are important marine coastal primary producers. Important factors influencing their distribution include light and temperature; despite kelp prime importance for ecosystem function, the molecular basis of these limitations is still poorly understood. In order to fill this gap we constructed a comprehensive cDNA library from RNA sampled under various light and temperature regimes as a basis for future studies about the mechanisms and pathways involved in acclimation to light and temperature stress in Saccharina latissima. A total of 400,503 ESTs was assembled into 28,803 contigs. We were able to assign putative functions or orthology relationships to more than 10,000 contigs either by BLASTx, Interpro protein motif annotation, or Gene Ontology. The most frequent Interpro protein domains found in the cDNA library were the protein kinase-like domain, serine/threonine-protein kinase-like domain, NAD(P)-binding and thioredoxin-like fold domain. Enzyme code (EC) annotation yielded in the attribution of 480 contigs, providing a total of 625 ECs, which could be mapped to 85 biochemical pathways. Comparative genomics of Saccharina latissima and Ectocarpus siliculosus revealed genome coverage of approximately 70% of our cDNA library, under the assumption of similar gene numbers in both species. GO term occurrence in S. latissima and E. siliculosus showed a similar distribution pattern among the root ontologies biological process, molecular function and cellular component. Comparative protein domain annotation of S. latissima und E. siliculosus showed that, probably due to the chosen stress conditions, the domains “thioredoxin fold”, “thioredoxin-like fold”, “heat shock protein 70”, and “bromoperoxidase/chloroperoxidase C-terminal” are over-represented in the cDNA library.

Description: Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have hitherto received little attention. Here we report the sequencing of the 105 Mbp genome of the florideophyte Chondrus crispus (Irish Moss) and the annotation of the 9,606 genes. The genome features an unusual structure, characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g. on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae, as well as adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (miRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, including a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis, showing the polyphyly of cellulose synthesis in Archaeplastida and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content we propose an evolutionary scenario which involves an ancestral red alga that was driven by early ecological forces to lose genes, introns and intergenetic DNA; this was followed by an expansion of genome size as a consequence of activity of transposable elements.