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.

为探究海水与淡水物种在盐度适应机制上的异同，我们对广盐性菌株MEM25与嗜中性淡水菌株FACHB-9的全球转录组及代谢组动态开展了比较分析。尽管二者的基因组序列共线性程度较高，但FACHB-9的转录组测序读段在MEM25基因组序列上的比对率极低，反之亦然。为缓解两物种基因注释质量差异所引入的偏差，我们采用了加权共表达网络分析（Weighted Correlation Network Analysis）。通过将每个直系同源组内的基因表达量进行整合以构建元基因表达水平，我们旨在捕捉反映共享功能角色的共表达模式，且不受每个基因家族内单个基因拷贝数的影响。