Journal Article

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

Jonathan H. Badger, Talina Konotchick, Christopher L. Dupont, Andrew E. Allen, Ruben E. Valas

2013

Overview

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.

• Publisher: New Phytologist Trust,Wiley Subscription Services, Inc,Wiley,Blackwell Publishing Ltd
• Subject: Algae / Annotations / BASIC BIOLOGICAL SCIENCES / biochemical pathways / biological models / Biological models (mathematics) / Brown algae / Cellular stress response / Cluster Analysis / comparative genomics / Complementary DNA / Depth / DNA / Ectocarpus / Ectocarpus siliculosus / ENVIRONMENTAL SCIENCES / Expressed Sequence Tags / Gene expression / Gene Expression Profiling / Gene families / Gene Library / Genes / Genomes / genomics / Kelp / Laminaria / Laminaria digitata / Libraries / Light / light harvesting complex / macroalgae / Macrocystis - genetics / Macrocystis - metabolism / Macrocystis - physiology / Macrocystis - radiation effects / Macrocystis pyrifera / Macrocystis pyrifera (giant kelp) / Markov chains / Model testing / Molecular Sequence Annotation / Nitrates / Nitrite reductase / nitrogen / Nucleotide sequence / Nutrients / Oceans and Seas / Open reading frames / Open Reading Frames - genetics / PCR / Phaeophyceae / Plant Sciences / Polymerase chain reaction / Proteins / quantitative PCR / quantitative polymerase chain reaction / Reductases / Ribosomal proteins / RNA / RNA, Messenger - genetics / RNA, Messenger - metabolism / RNA-Seq / Sea surface / Seasons / Sequence Analysis, DNA / Sequencing / Statistics as Topic / stress response / summer / Temperature / Transcription / transcriptomics / watercolumn gradients / water‐column gradients / winter