Abstract
Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.
Highlights
Ocean acidification is caused by the absorption of excessive anthropogenic CO2 emissions by the ocean
The underlying transcriptomic changes may help to maintain the physiological performance in response to elevated CO2
The Global Transcriptomic Response to Elevated pCO2 After Growing for 15 Generations ssRNA-seq data generated from the HC and LC physiological states were assembled and mapped
Summary
Ocean acidification is caused by the absorption of excessive anthropogenic CO2 emissions by the ocean. This study further revealed that genes in one CO2-responsive cluster share a putative cAMP responsive cis-regulatory sequence for a cAMP second messenger system (Hennon et al, 2015) These results imply that in addition to genes encoding central components of carbon fixation and assimilation, the response to elevated CO2 may involve a broader reprogramming of transcription, genome structure, and cell signaling. A total of 90% and 58% of TEs are long terminal repeat retrotransposons (LTR-RTs) in the P. tricornutum and T. pseudonana genomes, respectively. We have combined physiological performance measurements, with strand-specific RNA sequencing (ssRNASeq) to assess global transcriptomic changes in P. tricornutum in response to elevated pCO2 with respect to ambient pCO2 concentrations following growth for 15 generations. Our data provide new insights into how a diatom copes with elevated pCO2 using some potential epigenetic mechanisms and suggest an involvement of TEs and possibly lncRNAs in the acclimation response to elevated pCO2
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