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Carre, I.

Publications and source records attributed to Carre, I..

2 recordsLinked to original sources

Sensing the rainbow: genetic and physiological responses to light quality in Ostreococcus, an ecologically important photosynthetic picoeukaryote

Phytoplankton is exposed to dramatic variations in light quality as it moves up and down the water column or encounters the presence of sediments in the water. We investigated the potential impact on Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content and photophysiology after acclimation to monochromatic red, green or blue light. The clade B species RCC809, isolated from the deep Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves, and by increasing the relative level of blue-light absorbing pigments. In contrast, it responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originates from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton, and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning. HighlightWe characterise the effects of light quality on the transcriptome and photophysiology of Ostreococcus, a photosynthetic picoeukaryote, and show that responses are distinct between two ecotypes originating from different environments.

plant biology↗

RNA-Seq is not required to determine stable reference genes for qPCR normalization

Assessment of differential gene expression by qPCR is heavily influenced by the choice of reference genes. Although numerous statistical approaches have been proposed to determine the best reference genes, they can give rise to conflicting results depending on experimental conditions. Hence, recent studies propose the use of RNA-Seq to identify stable genes followed by the application of different statistical approaches to determine the best set of reference genes for qPCR data normalization. In this study, we demonstrate that the statistical approach to determine the best reference genes from randomly selected candidates is more important than the preselection of stable candidates from RNA-Seq data. Using a qPCR data normalization workflow that we have previously established; we show that qPCR data normalization using randomly chosen conventional reference genes renders the same results as stable reference genes selected from RNA-Seq data. We validated these observations in two distinct cross-sectional experimental conditions involving human iPSC derived microglial cells and mouse sciatic nerves. These results taken together show that given a robust statistical approach for reference gene selection, stable genes selected from RNA-Seq data do not offer any significant advantage over commonly used reference genes for normalizing qPCR assays.

molecular biology↗