A comprehensive cDNA library of light- and temperature-stressedSaccharina latissima(Phaeophyceae)

Abstract

Macroalgae of the order Laminariales (kelps) are important marine coastal primary producers with prime significance for ecosystem function. Important factors influencing their distribution include light and temperature but the molecular basis of kelp responses to these factors is poorly understood. We therefore 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 by BLASTx, Interpro protein-motif annotation, or Gene Ontology (GO). The most frequent Interpro protein domains found in the cDNA library were the protein kinase-like domain, serine/threonine-protein kinase-like domain, and NAD(P)-binding and thioredoxin-like fold domain. Enzyme code (EC) annotation yielded attributions for 480 contigs, providing a total of 625 ECs, which could be mapped to 85 biochemical pathways. Comparative genomics of S. latissima and Ectocarpus siliculosus indicated that our cDNA library gave a genome coverage of approximately 70%, assuming 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.

Transcriptomic Analysis of Acclimation to Temperature and Light Stress in Saccharina latissima (Phaeophyceae)

“…The cDNA library, featuring functional genome coverage of approximately 70%, was established from RNA sampled under various light and temperature regimes [120]. Original sequencing files of the cDNA library were uploaded at the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra; accession number SRR305166).…”

Herbivore-induced defence response in the brown seaweedFucus vesiculosus(Phaeophyceae): temporal pattern and gene expression

“…In general, annotation success is < 50% for brown algal genomic studies (e.g. Roeder et al, 2005;Wong et al, 2007;Pearson et al, 2010;Heinrich et al, 2012a) due to long 3′UTR sequences (Apt et al, 1995) and the evolutionary distance between heterokonts and available sequence data from other taxa used for comparisons (Pearson et al, 2010). The limited annotation success makes it difficult to identify candidate genes for defence induction, in particular since F. vesiculosus is a non-model organism without whole-genome sequencing.…”

Molecular and biochemical characterization of mannitol-1-phosphate dehydrogenase from the model brown alga Ectocarpus sp.

“…This was completed by analysis of publicly available raw RNA-seq data for Sp. japonica (Deng et al, 2012; SRA accession number SRX107054 and SRX107055), Saccharina latissima (Heinrich et al, 2012; SRA accession number SRX081375), and Macrocystis pyrifera (Konotchick et al, 2013; SRA accession numbers SRX220277, SRX220275, SRX220273, and SRX220272) that were cleaned-up through a custom made pipeline and assembled with CLC-assembly-cell. The presence of algal/apicomplexa M1PDH N-terminal module in other organisms was assessed by BlastP analysis against the non-redundant protein sequences database (http://www.uniprot.org/blast/).…”