Transcriptome profiling and co-expression network analysis of 96 Haematococcus pluvialis samples

Haematococcus pluvialis is a microalga known for producing the red carotenoid, astaxanthin. Key research areas to improve productivity include optimizing vegetative biomass, enhancing astaxanthin content, and controlling secondary cell wall formation. In this study, RNA-seq was conducted on 96 H. pluvialis samples under various treatments and time points, generating 96.7 GB of high-quality data (2,080,511,173 clean reads, quality score > 30). Gene expression was quantified as transcripts per million (TPM), and genes with similar expression patterns were clustered. A co-expression network, constructed with a soft threshold of β=7 (R² > 0.9), identified 39 co-expression modules, each averaging 732 genes. Additionally, the re-annotation process provided functional descriptions for around 8,600 previously uncharacterized genes. Gene functional classification analysis revealed their involvement in metabolic pathways related to genetic information processing and primary/secondary metabolite metabolism. This dataset provides a valuable resource for exploring the molecular mechanisms involved in critical processes such as growth regulation, astaxanthin accumulation, and secondary cell wall synthesis in H. pluvialis. Low-light cultivation stage: The algal cells were collected in the logarithmic phase (without any treatment, sample size: 3), the plateau phase (without any treatment, sample size: 3), and the plateau phase (1.8 g/L sodium acetate, sample size: 3).High-light stress cultivation stage:The algal cells were collected on the following days: the first day (without any treatment, sample size: 6), the first day (with 1 mM KI, sample size: 3), the first day (with nitrogen deprivation, sample size: 3), the first day (with nitrogen repletion, sample size: 3), the first day (with 1 mM fructose diphosphate, sample size: 3), and the first day (with 5 mM fructose diphosphate, sample size: 3); the second day(without any treatment, sample size: 3), the second day(with 0.5 g/L NaCl plus 0.5 mM CMP, sample size: 3); the Sixtieth hour(without any treatment, sample size: 3),the Sixtieth hour(Mutant, sample size: 3); the Third day(without any treatment, sample size: 9), the Third day(1 mM Xanthosine, sample size: 6), the Third day(with 1 mM taurine, sample size: 3); the Fifth day(without any treatment, sample size: 3),the Fifth day(1 mM KI, sample size: 3), the Fifth day(with nitrogen deprivation, sample size: 3),the Fifth day(nitrogen repletion, sample size: 3),the Fifth day(1 mM fructose diphosphate, sample size: 3),the Fifth day(5 mM fructose diphosphate, sample size: 3), the Fifth day(1 mM Uridine, sample size: 3), the Fifth day(1 mM Guanine, sample size: 3); the Tenth day(without any treatment, sample size: 3),the Tenth day(1 mM KI, sample size: 3).Harvest the algal cells, immediately freeze them in liquid nitrogen, and perform transcriptome sequencing. Each treatment had at least three biological replicates, resulting in a total of 96 sequencing samples.