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

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 durin...

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Autores principales: Konotchick, Talina, Dupont, Christopher L, Valas, Ruben E, Badger, Jonathan H, Allen, Andrew E
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Blackwell Publishing Ltd 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644879/
https://www.ncbi.nlm.nih.gov/pubmed/23488966
http://dx.doi.org/10.1111/nph.12160
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author Konotchick, Talina
Dupont, Christopher L
Valas, Ruben E
Badger, Jonathan H
Allen, Andrew E
author_facet Konotchick, Talina
Dupont, Christopher L
Valas, Ruben E
Badger, Jonathan H
Allen, Andrew E
author_sort Konotchick, Talina
collection PubMed
description 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.
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spelling pubmed-36448792013-05-06 Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season Konotchick, Talina Dupont, Christopher L Valas, Ruben E Badger, Jonathan H Allen, Andrew E New Phytol Research 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. Blackwell Publishing Ltd 2013-04 2013-03-13 /pmc/articles/PMC3644879/ /pubmed/23488966 http://dx.doi.org/10.1111/nph.12160 Text en Copyright © 2013 New Phytologist Trust http://creativecommons.org/licenses/by/2.5/ Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.
spellingShingle Research
Konotchick, Talina
Dupont, Christopher L
Valas, Ruben E
Badger, Jonathan H
Allen, Andrew E
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
title Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
title_full Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
title_fullStr Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
title_full_unstemmed Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
title_short Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
title_sort transcriptomic analysis of metabolic function in the giant kelp, macrocystis pyrifera, across depth and season
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644879/
https://www.ncbi.nlm.nih.gov/pubmed/23488966
http://dx.doi.org/10.1111/nph.12160
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