title: Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season.
abstract: To increase knowledge of transcript diversity for the giant kelp, Macrocystis 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 Markov models for c. 11% of open reading frames; M. pyrifera had highest similarity to other members of the Phaeophyceae, namely Ectocarpus siliculosus and Laminaria 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 LI818 (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.
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA.
authors.forename: Talina
authors.initials: T
authors.lastname: Konotchick
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Dupont
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA.
authors.forename: Ruben E
authors.initials: RE
authors.lastname: Valas
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA.
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Badger
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
mesh_terms: D016000:Cluster Analysis; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D008027:Light; D044662:Macrocystis / Q000235:genetics* / Q000378:metabolism* / Q000502:physiology / Q000528:radiation effects; D058977:Molecular Sequence Annotation; D009792:Oceans and Seas; D016366:Open Reading Frames / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012621:Seasons; D017422:Sequence Analysis, DNA; D013223:Statistics as Topic; D013696:Temperature
chemical_list: D012333:RNA, Messenger