| 1. |
- Chen, X. H., et al.
(author)
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Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy
- 2023
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In: Marine Life Science & Technology. - : Springer Science and Business Media LLC. - 2096-6490 .- 2662-1746. ; 5:1, s. 102-115
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Journal article (peer-reviewed)abstract
- Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic strategy. In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins, accounting for similar to 81% of the predicted protein-coding genes. Proteogenomic analysis identified 1235 novel genes, 975 revised genes, 104 splice variants and 234 single amino acid variants. Furthermore, our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions. These findings substantially improve the genome annotation of T. pseudonana and provide insights into new biological functions of diatoms. This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.
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| 2. |
- Gao, K. S., et al.
(author)
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Impacts of ocean acidification under multiple stressors on typical organisms and ecological processes
- 2020
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In: Marine Life Science & Technology. - : Springer Science and Business Media LLC. - 2096-6490 .- 2662-1746. ; 2:3, s. 279-291
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Journal article (peer-reviewed)abstract
- The oceans are taking up over one million tons of fossil CO2 per hour, resulting in increased pCO(2) and declining pH, leading to ocean acidification (OA). At the same time, accumulation of CO2 and other greenhouse gases is causing ocean warming, which enhances stratification with thinned upper mixed layers, exposing planktonic organisms to increasing levels of daytime integrated UV radiation. Ocean warming also reduces dissolved oxygen in seawater, resulting in ocean deoxygenation. All these ocean global changes are impacting marine ecosystems and effects are well documented for each individual driver (pH, oxygen, temperature, UV). However, combined effects are still poorly understood, strongly limiting our ability to project impacts at regional or local levels. Different regions are often exposed (and often adapted) to contrastingly different physical and chemical environmental conditions and organisms, and ecosystems from different parts of the world will be exposed to unique combinations of stressors in the future. Understanding the modulating role of adaptation, species niche and stressors' interaction is key. This review, being a non-exhaustively explored one, aims to provide an overview on understandings of ecophysiological effects of OA and its combination with covarying drivers, mainly warming, deoxygenation and solar UV radiation. We propose a testable hypothetical model as well as future research perspectives.
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