The bulk RNA-seq for Chlorella sp. MEM25 and Chlorella pyrenoidosa FACHB-9 under different salinity conditions
To investigate species similarities and differences in salinity adaptation mechanisms between saltwater and freshwater species, we conducted a comparative analysis of the global trancriptomic and metabolic dynamics of the euryhaline MEM25 and the neutrophilic freshwater FACHB-9. Despite the relatively high synteny observed in their genome sequences, there was a remarkably low alignment ratio of FACHB-9 transcriptomic reads on MEM25 genome sequences, and vice versa. To mitigate biases stemming from differences in gene annotation quality between the two species, we employed a Weighted Correlation Network Analysis. By aggregating the expression of genes within each orthogroup to create a metagene expression level, we aimed to capture co-expression patterns reflective of shared functional roles, irrespective of individual gene copy numbers within each gene family.