Transcriptomic analysis of metabolic function in the giant kelp, M acrocystis pyrifera , across depth and season

Summary To increase knowledge of transcript diversity for the giant kelp, M acrocystis pyrifera , and assess gene expression across naturally occurring depth gradients in light, temperature and nutrients, we sequenced four cDNA libraries created from blades collected at the sea surface and at 18 m depth during the winter and summer. Comparative genomics cluster analyses revealed novel gene families (clusters) in existing brown alga expressed sequence tag data compared with other related algal groups, a pattern also seen with the addition of M . pyrifera sequences. Assembly of 228 Mbp of sequence generated c . 9000 isotigs and c . 12 000 open reading frames. Annotations were assigned using families of hidden M arkov models for c . 11% of open reading frames; M . pyrifera had highest similarity to other members of the P haeophyceae, namely E ctocarpus siliculosus and L aminaria digitata . Quantitative polymerase chain reaction of transcript targets verified depth‐related differences in gene expression; stress response and light‐harvesting transcripts, especially members of the LI 818 (also known as LHCSR ) family, showed high expression in the surface compared with 18 m depth, while some nitrogen acquisition transcripts (e.g. nitrite reductase) were upregulated at depth compared with the surface, supporting a conceptual biological model of depth‐dependent physiology.