Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
Article first published online: 13 MAR 2013
© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust
Volume 198, Issue 2, pages 398–407, April 2013
How to Cite
Konotchick, T., Dupont, C. L., Valas, R. E., Badger, J. H. and Allen, A. E. (2013), Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season. New Phytologist, 198: 398–407. doi: 10.1111/nph.12160
- Issue published online: 20 MAR 2013
- Article first published online: 13 MAR 2013
- Manuscript Accepted: 10 DEC 2012
- Manuscript Received: 12 SEP 2012
- National Science Foundation. Grant Numbers: NSF-OCE-1136477, NSF-MCB-1024913, DOE-DE-SC0006719
- Beyster Foundation
- comparative genomics;
- light harvesting complex;
- Macrocystis pyrifera (giant kelp);
- quantitative PCR;
- water-column gradients
- 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.