Premium
Transcriptomic analysis of metabolic function in the giant kelp, M acrocystis pyrifera , across depth and season
Author(s) -
Konotchick Talina,
Dupont Christopher L.,
Valas Ruben E.,
Badger Jonathan H.,
Allen Andrew E.
Publication year - 2013
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.12160
Subject(s) - macrocystis pyrifera , biology , kelp , open reading frame , transcriptome , gene , genetics , botany , evolutionary biology , gene expression , peptide sequence
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.