GSE202896
Quantitative Analysis of Phaeodactylum tricornutum transcriptomes
Purpose: Using RNAseq to profile transcriptomes to compare wildtype and PtTryp2 knockout lines across different nutrient conditions, aim to further explore the molecular function of PtTryp2 in regulating cell growth and responses to N- and P-stress. Methods: Libraries for RNAseq were created from 1µg of mRNA from each culture. The resulting libraries were loaded into the patterned nanoarray, and single-end 50 bp reads were generated on BGIseq500 platform (BGI-Shenzhen, China), with a data output of about 22 M total clean reads for each library. Results: Transcriptomic data show that PtTryp2 knockout led to the upregulation of most of the nitrogen assimilation and metabolism genes under both N-depleted and replete conditions. In addition, when comparing N-depleted with N-replete conditions, 646 differentially expressed genes (DEGs) were identified in the blank vector control (KOC) but only 187 in PtTryp2-KO1, considerably fewer in the knockout mutant. Based on RNA-seq, remarkably more DEGs were found for the P-depleted versus nutrient-replete comparison in PtTryp2-KO1 (1501) than that in KOC (277). Besides, in PtTryp2-KO1, the majority of these DEGs (77.25%) exhibited greater fold changes than that in KOC. Conclusions: Transcriptomic data coupling with physiological experiments, suggesting that PtTryp2 knockout led to amplitude magnification of the NO3- and Pi uptake “seesaw”, whereas PtTryp2 overexpression dampened it. All our data demonstrate in concert that PtTryp2 is a coordinate regulator of N-P stoichiometric homeostasis. Overall design: RNA-seq profiles of 18 Phaeodactylum tricornutum cell samples.