ArticleThe New phytologist2013
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season.
Article in The New phytologist, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- Insights from farming Macrocystis pyrifera offshore: phenotypic analysis, genome-wide association studies, genomic selection.Heredity · 2026Article
- Insights from farmingbioRxiv : the preprint server for biology · 2025Article
- A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera).BMC genomics · 2023Article
- Insight into the genome data of commercially important giant kelpData in brief · 2022Article
- Effect of environmental history on the habitat-forming kelp Macrocystis pyrifera responses to ocean acidification and warming: a physiological and molecular approach.Scientific reports · 2021Article
- First Draft Genome Assembly of the SeaweedFrontiers in genetics · 2020Article
- Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima?BMC plant biology · 2019Article
- Transcriptional Shifts Highlight the Role of Nutrients in Harmful Brown Tide Dynamics.Frontiers in microbiology · 2019Article
- Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant KelpFrontiers in microbiology · 2018Article
- Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae.Frontiers in microbiology · 2017Article
- A two-component nonphotochemical fluorescence quenching in eustigmatophyte algae.Photosynthesis research · 2017Article
- A kelp with integrity: Macrocystis pyrifera prioritises tissue maintenance in response to nitrogen fertilisation.Oecologia · 2016Article
- Infection of the brown alga Ectocarpus siliculosus by the oomycete Eurychasma dicksonii induces oxidative stress and halogen metabolism.Plant, cell & environment · 2016Article
- Tipping points in seaweed genetic engineering: scaling up opportunities in the next decade.Marine drugs · 2014Review
- De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms.Frontiers in microbiology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.